Briefing for the New President: The Terrorist Threat in Indonesia and Southeast Asia
Briefing for the New President: The Terrorist Threat in Indonesia and Southeast Asia
Indonesia's Police: The Problem of Deadly Force
Indonesia's Police: The Problem of Deadly Force
Op-Ed / Asia 19 minutes

Briefing for the New President: The Terrorist Threat in Indonesia and Southeast Asia

Counterterrorism capacity in Southeast Asia is improving, reducing the likelihood of a major attack on Western targets in the near term. However, jihadi ideology has taken root in Indonesia, and while the region’s largest terrorist organization, Jemaah Islamiyah, appears to be more interested in rebuilding than mounting operations, its members still constitute an important recruitment pool for other groups. Most Indonesian jihadis appear to be more focused on local than foreign targets, but that focus can aid recruitment and facilitate alliances with other organizations. While the Iraq insurgency has not attracted Southeast Asian participation, the resurgence of the Taliban on the Afghan-Pakistan border could. The United States, under the next president, could help develop better information sharing between South and Southeast Asia. Southeast Asia may not be the “second front” that many feared after the first Bali bombs, but the terrorism threat in the region has not gone away.

Southeast Asia holds many encouraging signs on the counterterrorism front, particularly in Indonesia, where the short-term likelihood of another suicide bombing aimed at Western targets appears low. Long-term prospects, however, are more worrying.

Southeast Asia’s most notorious jihadi organization, the Indonesia-based Jemaah Islamiyah (JI), is largely dormant but far from dead. Its leadership is not interested in Western targets, but its members still constitute a potentially important recruitment pool for other terrorist groups.

Noordin Top, the Malaysian national who heads the splinter group of JI responsible for major anti-Western bombings in 2003, 2004, and 2005, remains at large in Indonesia. His capacity to mount another attack appears low, but his capacity for recruitment should not be discounted. It is worth noting that two of his key aides were released from prison in 2007.

Most other known Indonesian jihadi groups appear to be more interested in stirring up communal tensions than in attacking the United States and its allies; “Christianization” is seen as the bigger threat.

Counterterror capacity in the region is improving; the Indonesian police have made particularly impressive gains.

International funding for jihadi operations has largely dried up.

These developments notwithstanding, jihadi ideology has taken root and has spread beyond the groups known to have used violence in the past. Some thirty JI-affiliated schools continue to educate the children and younger siblings of JI members and recruit new leaders for the organization. Contacts with South Asia continue, particularly in Pakistan and Bangladesh, but they are poorly monitored or understood; the Taliban resurgence on the Pakistan-Afghan border eventually could draw in Southeast Asians. While militants in southern Thailand continue to operate without any significant outside assistance, interest in that conflict appears to be increasing among some Indonesian jihadis. A small number of Indonesians from several different groups continue to operate in the Philippines, but some of those on the U.S. most-wanted list appear to be trying to return home. Above all, it is important to underscore that the jihadi movement is dynamic, always evolving, adapting, and mutating. JI is important but the greater danger may lie in groups or individuals, perhaps now unknown, that may emerge and be able to draw on dissatisfied members of JI and other organizations.

Jemaah Islamiyah

JI has shrunk steadily since the first Bali bombing in October 2002. Once an organization that spanned five countries (Indonesia, Malaysia, Singapore, Philippines, and Australia), its administrative structure in late 2007 covered Indonesia only, its al Qaeda links and international funding were largely gone, hundreds of its members were in prison across the region, and many others were cooperating with police and intelligence, some of them overtly. The organization’s leaders were known to be opposed to al Qaeda–style bombings on Indonesian soil, not so much because they were illegitimate but because they were counterproductive—attacks on Western targets killed more Indonesians than infidels, provoked community outrage, and led to mass arrests.

From mid-1999 on, JI’s attacks on civilians were controversial within the organization, except in Ambon and Poso, two areas where local Muslims were being killed in communal fighting. Initiated by Hambali, an Indonesian citizen now in Guantanamo, and supported financially by al Qaeda, operations such as the 2000 Christmas Eve bombings and Bali I were conducted by ad hoc teams operating outside JI’s formal structure and sometimes without the knowledge of senior leaders. These teams drew largely on members of Mantiqi I, the JI division covering Malaysia and Singapore, based at an Islamic boarding school (pesantren) in Johore; the strongest opposition came from leaders in Indonesia where the attacks took place (Jones 2005, 169-70). It is no coincidence that after Hambali’s arrest, Noordin Mohammed Top, a Malaysian who had been the school’s nominal director, continued the attacks, working largely with Indonesians who had studied or taught there. Noordin’s attacks on the Marriott Hotel (2003), the Australian embassy (2004), and Bali II (2005) were not endorsed by the JI leadership, although individual members provided logistical help, and Noordin began calling his group “Al-Qaeda for the Malay Archipelago.” Noordin’s main ideological mentor was Ali Ghufron alias Mukhlas, on death row since 2003 for his role in Bali I (International Crisis Group 2006, 1).[fn]See International Crisis Group (2006). Mukhlas was arrested in 2002, tried, and sentenced to death in 2003.Hide Footnote While most JI leaders consider Noordin and his men as a separate group, they have generally been willing to offer him protection, perhaps since 2005, in exchange for a promise to refrain from attacks. He, however, may consider himself the “real” JI, since Mukhlas, writing from prison in 2005, castigated those who sit on their hands while others pursue jihad (Aly Ghufron 2004).[fn]After the second Bali bombing on October 1, 2005, police discovered that Noordin Top’s associates had developed a Web site specifically to disseminate jihadi teachings from al Qaeda sites. Several Indonesians were also contributors, including Aly Ghufron alias Mukhlas, one of the masterminds of the first Bali bombing. The site,, was subsequently shut down.Hide Footnote The sense of JI having become dull and do-nothing led some JI members to join Noordin in early 2005, and others may follow by joining his group or other splinters.

Military Capacity

JI retains a structure with at least nine hundred inducted members and likely more across Indonesia with other individual members, largely cut off from the structure, in Malaysia and the Philippines (International Crisis Group 2007b). An intricate web of kinship, friendship, school, military training, and business ties, combined with the obedience and loyalty imposed by the induction pledge, keeps the organization together despite the many arrests and a number of ideological fissures. (After Noordin broke away, the most important split is between those who believe JI should remain clandestine and those who believe its members should be free to join above-ground organizations to work for the implementation of Islamic law.)[fn]One of these aboveground organizations is Majelis Mujahidin Indonesia, led by Abu Bakar Ba’asyir, that includes many Jemaah Islamiyah (JI) members among its ranks.Hide Footnote Its leadership still draws heavily on those trained in Afghanistan in the late 1980s and early 1990s. Many of the “Afghan alumni” are working with the police, however, and most of the rest are not disposed toward attacks on Western targets—and in any case their skills are rusty.

More problematic are the Mindanao-trained cadres who fought in Ambon and Poso. About five fled to Java after police operations in Poso in January 2007 and have gone underground; they are unlikely to be content living quietly as religious scholars. Several expert bomb makers also remain at large, and access to explosives and/or small arms is not particularly difficult.[fn]These include Reno alias Tedi, believed to be a Darul Islam member, who apprenticed himself to Dr. Azhari Husein and escaped when police killed Azhari in November 2005; and Taufik Bulaga, also known as Upik Lawanga, a local Poso recruit, who learned bomb making from another of Azhari’s proteges.Hide Footnote JI tries to maintain weapons caches—military readiness is an important element of its jihadi doctrine—but the firearms and bombs found in March 2007 were sealed in a concrete bunker and clearly not planned for immediate use.

While Noordin’s group in particular has discussed the possibility of other forms of attacks—targeted assassinations and hostage taking, for example—former JI members say that these require at least as much planning as bomb attacks, and the few men with a known capacity to work out the logistics of complicated operations are mostly dead or in custody. Assassinations were a standard part of the jihadi repertoire in Poso and Ambon, however, and it is not impossible that JI could make attempts elsewhere.

The big exception to the generally low military capacity of jihadi groups at present lies with the small group of Indonesians and a few other Southeast Asians in Mindanao working with the Abu Sayyaf group. That group includes two of the Bali I bombers, Umar Patek and Dulmatin, both JI members but ones more associated with Hambali’s “nonstructural” operations than with the JI organization per se and now closer to the organization KOMPAK than JI. Both men have come close several times to being captured or killed in the past two years and are said to be looking for ways to return to Indonesia. If they did, they would have instant legitimacy as commanders with up-to-date combat experience and could inject new zeal into the jihadi movement, either by joining Noordin or leading a new splinter. Both reportedly would like to help out in southern Thailand, although the Thai militants have shown no interest in outside assistance.[fn]The Thai insurgency is an ethnonationalist movement that builds on resentment of a Muslim Malay minority against a Thai Buddhist majority. Much of the recruitment takes place in Muslim schools, led by teachers, including many trained abroad. But the pull is nationalism, not global jihad. BRIEFING FOR THE NEW PRESIDENT 77Hide Footnote Nevertheless, if they did return to Indonesia, efforts to bolster links between Indonesian and Thai jihadi groups could increase.


No significant external funding has come into JI since 2003 when a cell in Karachi arranged a transfer through al Qaeda contacts. Many factors indicate that the organization itself is strapped for funds; would-be participants in a JI training project for ex-prisoners scheduled for late 2007 in central Java were told that they would have to pay their own way. JI members arrested in March 2007 said the major source of funding was infaq, or contributions from members, generally monthly but based on ability to pay. Larger donations come from sympathetic businesses, some but not all JI-owned. In 2005 and 2006, JI members in Poso relied on fa’i, robbing of non-Muslims to support jihad, as did Noordin for the Bali II attack. Donors in Saudi Arabia and elsewhere in the Gulf have provided funding to Indonesian jihadi groups in the past, particularly at the height of the Ambon and Poso conflicts, but those donations do not appear to be significant for defraying day-to-day operating expenses.


A few Indonesians are still reaching Mindanao for training but on a very sporadic basis; the Moro Islamic Liberation Front is no longer a friendly host of foreign jihadis, although a few commanders in the Pawas area outside Cotabato may not have gotten the message. Increased vigilance and border controls mean that it is increasingly difficult to use the usual transit routes from North Sulawesi to Mindanao or up the coast of East Kalimantan to Sabah to Mindanao. A third, less patrolled route, from the island of Morotai off the coast of Halmahera in North Maluku, Indonesia, directly to the Mindanao coast apparently gets some traffic, but it has never been preferred because of the longer stretches of open sea. Arrests of members of JI’s military wing in early 2007 revealed that the only training they received was little more than periodic outings in nearby hills, with rare opportunities to use real weapons. The reemergence of a regional jihadi training center of any size or sophistication would be a source of grave concern, but for the moment, there is not a plausible candidate.

Many factors indicate that [Jemaah Islamiyah] is strapped for funds.

As of 2007, no evidence showed that any Southeast Asians had trained with Iraqi insurgents. The place to watch is the border area between Pakistan and Afghanistan. Hundreds of Southeast Asian, mostly Indonesian, jihadis trained there between 1985 and 1994, with a few dozen more going to Afghanistan for short courses between 1999 and 2001. A JI cell operated out of Karachi through September 2003, and Indonesian jihadis from a number of different organizations have well-established contacts in Karachi, Lahore, Peshawar, and Waziristan. Many students find their ways to madrasahs with private funding, and a steady stream of Indonesians travel to India, Pakistan, and Bangladesh every year to join gatherings of Tablighi Jamaat, a nonpolitical Islamic missionary organization that has been used as cover by jihadis, particularly for international travel. Unless Southeast Asians register with their embassies, their governments are likely to have little capacity to monitor their whereabouts or activities. That said, in the late 1980s and early 1990s, the training of Southeast Asians along the Afghan border was made possible by factors absent in 2008: virtually unlimited funding from the Saudis; logistical assistance in Malaysia, through the Indonesian exile group that became JI; and tacit support or unconcern from much of the international community.

Local Targets

Most of the jihadi groups in Indonesia are more focused on local Christians and thaghut (anti-Islamic) officials as enemies than on the United States, although in their view, the United States, as leader of the international Crusader-Zionist alliance aimed at destroying Islam, is ultimately responsible for all ills. The focus on Christians stems from several factors: a sense from Salafi jihadi interpretation of the Koran that Jews and Christians are the natural enemies of Islam,[fn]Salafi Muslims try to emulate the practices of the Prophet Mohammed and his companions, believing that seventh-century Islam was the purest. Salafi jihadis add to that puritanism a belief that jihad, in the sense of actual physical war, is necessary to fight Islam’s enemies and establish an Islamic state. The former see the latter as too political and religiously misguided; in many countries where a local jihad is being waged, “pure” salafis are the most vocal opponents of salafi jihadis.Hide Footnote the conviction that Christians will again attack Muslims as they did in Ambon and Poso unless they are “taught a lesson,” the limited success of aggressive Protestant evangelical movements in converting Muslims and the fear of a wider effort at “Christianization,” and the fact that several of the top officers of the police counterterrorist team are Christians.

The branding of Indonesian officials as thaghut is based in part on their participation in a political system based on man-made rather than sharia or Godgiven law. But it is also based on a reading of radical tracts, translated from the Arabic and widely circulated in Indonesian jihadi circles, accusing Muslim governments such as Saudi Arabia and Egypt of selling out to Americans. Indonesian readers are tacitly invited to make the obvious analogy. The two leading ideologues in this respect are Abu Muhammad al-Maqdisi, released from a Jordanian prison in early 2008, and Abdul Qadir bin Abdul Aziz, now in prison in Egypt.[fn]Al-Maqdisi is known in Indonesia as the mentor of the late Abu Musab al-Zarkawi in Iraq, but he distanced himself from Zarkawi’s methods and wrote a tract from prison criticizing suicide bombing and indiscriminate attacks on civilians. The Indonesian translation of that text was published in late 2007 under the title Mereka Mujahid tapi Salah Langkah (They’re Mujahidin but They Are Making Mistakes) and is said to be a bestseller in jihadi circles.Hide Footnote

Although Western governments are generally less interested in jihadi groups when those groups do not have foreigners in their sights, they should be more attentive for several reasons.

The focus on local kafir, or infidels, can give jihadi groups a reason to continue at a time when resources to join the global jihad are lacking.

The issue of apostasy at home—Christian organizations converting Muslims—can generate far more fury than civilian deaths in Iraq or Afghanistan, and that fury can then be redirected at the alleged source of funding and support for these organizations: the United States.

Local jihads such as Ambon and Poso have been hugely important for recruitment and combat training, and experience in local operations makes attacks on a larger scale more thinkable.

Assassination of top government officials, if the focus on thaghut officials should ever lead to that, would have far more serious political repercussions for Indonesia than another attack on a bar or restaurant.

Focus on local targets provides an ideological meeting ground between radical jihadi groups and Islamist groups not involved in terrorism.

Groups with a local agenda always can be taken on as partners by those with a more international outlook.

We know of five or six such groups in Indonesia alone, and there are probably more.[fn]These include KOMPAK, an Islamic charity with a militia that was active in Ambon and Poso and whose veterans can be quickly mobilized; Ring Banten in West Java; Mujahidin Kayamanya in Poso, a KOMPAK ally; Laskar Jundullah in Makassar; (a different) Laskar Jundullah in Solo; and Jama’ah Tauhid wal Jihad in Bandung.Hide Footnote The most urgent task to prevent the growth of these organizations is to develop a watch list of areas with serious communal tensions (often originating in local political power struggles or land disputes rather than religious issues) and work to reduce them. Two such areas, in addition to Poso, are Mamasa in West Sulawesi and Manokwari in West Papua.

Prisons and the Legal System

Southeast Asian governments, like their counterparts elsewhere, are belatedly realizing that prisons have to be included as a focus of counterterrorism strategies. Indonesia does not have—and should not be encouraged to develop—an Internal Security Act that permits indefinite preventive detention. A 2003 counterterrorism law allows terrorism suspects to be kept for a week, after which they have to be charged or released. Those charged are tried fairly quickly, in trials that are fully open to the public and media and that, while not always competently prosecuted, are generally fair. Intimidation of judges and prosecutors by jihadi groups has been a problem, particularly in Poso; police have also sometimes intervened with judges to try to get lenient sentences for men who have cooperated or who are seen as key to the police de-radicalization program. This is discussed further below.

Since the first Bali bombs in October 2002, some four hundred suspects have been arrested. Of these, close to three hundred—all but one of them men—have been brought to trial. Many have been released after serving their sentences, some sixty in 2006 and 2007 alone, including some senior JI leaders. What happens inside prison, in terms of recruiting ordinary criminals and prison guards and dissemination of jihadi ideology, thus becomes critical, as does what happens after release. Government capacity for monitoring these processes, however, remains very low. The problem in Indonesia is less radicalization through illtreatment and poor prison conditions than ongoing indoctrination through uncontrolled radical discussion and study groups, the use of cell phones, and links to the local jihadi publishing industry. Much of the translation from Arabic into Indonesian of material on international jihadi Web sites is undertaken by prisoners with the requisite language expertise—and time on their hands. Visitors bring the printouts and collect the finished translations, often written out in longhand. They either post them on local jihadi Web sites or provide them to companies linked to the major jihadi groups, and often do both.

Prisons are also a factor in the constant mutation of jihadi groups. New alliances as well as new fissures can form there. Influential leaders can lose their authority and others can rise, depending on their access to cash. In JI, ex-prisoners generally are not permitted to return to formal leadership positions because of their exposure; a clandestine organization needs “sterile” commanders. The problem is that fewer and fewer such men in the pipeline have the appropriate combination of military training and religious knowledge.

Police have embarked on a prisoner-focused “de-radicalization” program aimed at persuading jihadis to reject the use of terrorist tactics. A key element is provision of economic aid, usually to prisoners’ families and often involving school fees for children, on the assumption that acceptance of aid from the police entails a rejection of the jihadi premise that all officials are thaghut. If jihadis are willing to take money from police, the thinking goes, they may be ready to question other jihadi teachings. By late 2007, some twenty-five Afghan-trained JI members were cooperating with the police. Most were opposed to al Qaeda–style bombings in Indonesia from the outset, so it is not clear that the availability of aid changed many minds. Rather, it provided a powerful incentive for prisoners to cooperate with the police and helped to create new divisions between “collaborationists” and “purists.” While police clearly hope that those members will return to their communities and help discourage recruitment into terrorist cells, there appears to be little strategic thinking thus far about how this might be accomplished. They have also made little headway in persuading the seriously hardcore ideologues of the movement to change their views (International Crisis Group 2007a). That said, no other agency in the Indonesian government is giving serious thought to how to address homegrown extremism, and the police deserve credit for doing so.

New Groups

While the best-known jihadi groups are in a state of some disarray, efforts appear to be under way to organize new ones, in a way that could have repercussions a few years hence. Al-Muhajirun, the international jihadi group that broke away from Hizb ut-Tahrir, for some time has maintained an Indonesian Web site, but over the past two years, it appears to have become more active in recruiting members. In 2006 it produced two issues of a magazine that then collapsed, presumably for lack of funding. It appears to recruit from Salafi schools; its leader, Abu Yahya, is a former Hizb ut-Tahrir Indonesia (HTI) member. Individuals from a Darul Islam faction in Central Java, who are close to the leader of the Bandung-based Jama’ah Tauhid wal Jihad, reportedly have been making overtures to JI and KOMPAK members about the possibility of forming a new organization.

Some ex-prisoners, marginalized by their organizations because of their exposure, could find a new home there if the new group were to take off. In Makassar, newly released members of Laskar Jundullah could become the nucleus of a revived jihadi effort in Sulawesi. The biggest mistake for analysts of the region would be to draw conclusions about the nature of the security threat from an analysis of the current state of JI alone.

Policy Recommendations

In general, a new president could perform a useful service by downplaying the importance of counterterrorism in U.S. policy without cutting back on the level of international aid support to nations that currently receive it. A widespread belief throughout the region is that the Bush administration viewed all developments in the region through a counterterror lens to the point that even its flagship project of assistance to Indonesian education was seen less as an important development program in its own right than (misguidedly) as a way of reducing the potential for radical recruitment. Indonesia and other governments in the region do not see countering terror as their number one priority, so it is important that the United States be seen as restoring some perspective in its foreign policy.

That said, U.S. counterterrorism assistance in Indonesia, focused on increasing the capacity of police and courts to investigate and prosecute terrorism, has been effective and should be continued. In particular, its assistance to two units of the police, Detachment 88 and the Bomb Task Force, together with support from the Australian Federal Police, has been instrumental in Indonesia’s success in apprehending many terrorist suspects since 2002.

The United States is supporting a Terrorism and Transnational Crimes Task Force within the attorney general’s office to train prosecutors, as well as more general assistance to police through the Department of Justice’s International Criminal Investigative Training Assistance Program (ICITAP). Both address important issues, although a thorough audit and evaluation of all counterterrorism assistance is probably in order to see what elements worked better than others and why and where significant wastage occurred.

A new administration could help develop better information sharing between South and Southeast Asia, through supporting exchange programs of police and intelligence officers and relevant government agencies and strengthening understanding of South Asian militant Islamic networks and their linkages to Southeast Asia.

For Indonesia in particular, U.S. assistance designed to monitor and effectively address communal tensions across the country would be useful. In addition to serving a more general conflict-prevention objective, the goal should be to understand when and how radical groups move in to exploit these tensions. In this context, it would also be useful to better understand the relationship between activities of Christian evangelical movements and the emergence of radical Muslim backlash.

In some key areas, aid is needed but the United States is poorly placed to assist. One is prison reform, where the need is urgent but the profile of abuses at Abu Ghraib and Guantanamo remains so high that other donors would be more effective.

The new president needs to understand that jihadi groups in Indonesia are in a state of flux, meaning their capacity for undertaking terrorist attacks is constantly changing. Southeast Asia at the moment may not be the “second front” that many feared after the first Bali bombs, but no one should be complacent in the belief that attacks on Westerners are history.

Sidney Jones is senior adviser to the International Crisis Group’s Asia program. She previously was a Ford Foundation program officer (1977-1984) in Jakarta and New York; Amnesty International researcher on Indonesia, the Philippines, and the Pacific (1985-1988); and Asia director of Human Rights Watch (1989-2002). She holds degrees from the University of Pennsylvania in oriental studies and international relations and in 2006 received an honorary doctorate from the New School in New York. She has written extensively on conflict, radical Islam, terrorism, and human rights in Southeast Asia, with a particular focus on Indonesia.


Al-Maqdisi, Abu Muhammad. 2007. Mereka Mujahid Tapi Salah Langkah. Solo, Indonesia: JAZERA Press.

Aly Ghufron. Wasiat dan Pesan-Pesan untuk Kaum Muslimin. (closed 2005).

International Crisis Group. 2006. Terrorism in Indonesia: Noordin’s networks. Asia Report no. 114, May 5

International Crisis Group. 2006. 2007a. “Deradicalisation” and Indonesian prisons. Asia Report no. 142, November 19.

International Crisis Group. 2006. 2007b. Indonesia: Jemaah Islamiyah’s current status. Asia Briefing no. 63, May 3.

Jones, Sidney. 2005. The changing nature of Jemaah Islamiyah. Australian Journal of International Affairs 59 (2): 169-78.

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