Nine years after the first U.S. drone strike in Pakistan’s Federally Administered Tribal Areas (FATA) in 2004, the U.S. refuses to officially acknowledge the CIA-run program, while Pakistan denies consenting to it. This secrecy undermines efforts to assess the program’s legality or its full impact on FATA’s population. It also diverts attention from a candid examination of the roots of militancy in the poorly governed tribal belt bordering southern and eastern Afghanistan and how best to address them. Drone strikes may disrupt FATA-based militant groups’ capacity to plan and execute crossborder attacks on NATO troops and to plot attacks against the U.S. homeland, but they cannot solve the fundamental problem. The ability of those groups to regroup, rearm and recruit will remain intact so long as they enjoy safe havens on Pakistani territory and efforts to incorporate FATA into the constitutional mainstream are stifled.

Since 2004, there have been at least 350 drone strikes in FATA, mostly in North Waziristan, South Waziristan and Kurram agencies. These have killed significant numbers of al-Qaeda leaders and senior militant commanders of both the Pakistani and Afghan Taliban, but also scores of innocent civilians, in part because of so-called “signature” strikes that target groups of men based on behaviour patterns associated with terrorist activity rather than known identities.

Even with so-called “personality” strikes in which the individual has been targeted based on evidence of identity, accurate assessments of collateral damage are impossible. Independent researchers, facing significant military and militant-imposed barriers to access in FATA, rely primarily on media reports that depend largely on anonymous U.S. government and/or Pakistani military sources – each with a vested interest in under- or over-reporting civilian casualties.

Neither is it possible to gauge the real feelings of civilians who live in the areas of drone operations. Fearing retaliation from the militants or the military, respondents choose their words carefully. For the same reasons, it is hard to determine with any precision the strategic impact of the drone campaign. While reported signature strikes may in particular fuel local alienation, at the same time, the deaths of senior, highly experienced commanders are certainly a hard blow for the militants.

Pakistan’s attitude towards drones borders on the schizophrenic. Rather than inherently opposing the strikes, its leadership, in particular its military, seeks greater control over target selection. This is often to punish enemies, but sometimes, allegedly, to protect militants who enjoy good relations with, or support from, the military – leaders of the Haqqani network, for example, or some Pakistani Taliban groups with whom the military has made peace deals.

Ample evidence exists of tacit Pakistani consent and active cooperation with the drone program, contradicting the official posture that it violates the country’s sovereignty. This includes acknowledgements by former President Pervez Musharraf in April 2013 and by then-Prime Minister Yousuf Raza Gilani in 2008 and 2010. After the October 2001 U.S.-led intervention in Afghanistan, Musharraf’s military regime permitted a substantial CIA presence in at least two airbases, Shamsi in southern Balochistan and Shahbaz in Sindh’s Jacobabad district, for intelligence gathering and collaboration; both were used to gather intelligence for drone strikes and possibly even to conduct them. This cooperation and collaboration signified Pakistan’s assent to the program. It was not until the November 2011 NATO air raid that killed 24 Pakistani soldiers near the Afghan border and months after the U.S. raid that killed Osama bin Laden in Abbottabad, vitiating relations with Washington, that Islamabad demanded the U.S. vacate one of the bases.

While drones have not themselves caused the political falling out between Washington and Islamabad, the Pakistani military has attempted to take advantage of downturns in the relationship to leverage greater control over drone targets. Even after the U.S. vacated the Shamsi base in December 2011, some level of Pakistani sanction for the strikes continues. While condemning attacks against its anti-Afghanistan-oriented jihadi allies, such as the August 2012 killing of Badruddin Haqqani, the Haqqani network’s third in command, it supports strikes against its internal enemies, such as Maulvi Dadullah, the leader of the Pakistani Taliban in Bajaur Agency, killed in a drone strike in Afghanistan’s Kunar province that same month. The U.S. hit list now reportedly includes Mullah Fazlullah, the leader of a Pakistani Taliban faction in Khyber Pakhtunkhwa’s (KPK’s) Malakand region, ousted in a military operation in 2009, and now operating out of Afghanistan’s Nuristan province.

The legal debate does not pivot only on Pakistani consent. Both countries are subject to numerous obligations under international law and their respective domestic legislation. Islamabad has a constitutional and international obligation to protect the lives of citizens and non-citizens alike on its territory. Even if it seeks U.S. assistance against individuals and groups at war with the state, Pakistan is still obliged to ensure that its actions and those of the U.S. comply with the principles, among others, of distinction and proportionality under International Humanitarian Law, and ideally to give independent observers unhindered access to the areas targeted.

The Obama administration should terminate any practice, such as the reported signature strikes, that does not comply with principles of international humanitarian and human rights law. It must also introduce transparency to the drone program, including its governing rules, how targets are selected and how civilian damage is weighed. By transferring its management from the CIA to the Defense Department, the administration would establish clearer lines of authority and accountability, including greater congressional and judicial oversight.

Distorted through hyper-nationalistic segments of the Pakistani media and hijacked by political hardliners, the domestic Pakistani debate on the impact of drone operations has overshadowed a more urgent discussion about the state’s obligation to its citizens in FATA, who are denied constitutional rights and protections. In the absence of formal courts and law enforcement institutions, the state fails to protect FATA’s residents from jihadi and other criminal groups.

The core of any Pakistani counter-terrorism strategy in this area should be to incorporate FATA into the country’s legal and constitutional mainstream. This should be accompanied by a national counter-terrorism policy that prioritises the modernisation of a failing criminal justice sector, thus enabling the state to bring violent extremists to justice.

While the U.S. and international debate over legitimacy and control of drone strikes is highly important, drones are not a long-term solution to the problem they are being deployed to solve – destruction of local, regional and wider transnational jihadis who operate out of Pakistan’s tribal belt.

The U.S. policy should be two-fold: pressuring the Pakistan military to abandon any logistical or other support to violent extremists, including by more rigorously applying existing conditions on security assistance; and encouraging and supporting efforts by the elected leadership in Islamabad to extend the state’s writ to FATA. Similarly, if Pakistan is genuinely committed to ending strikes on its territory, it should realise that its strongest case against the U.S. drone program lies in over-hauling an anachronistic governance system so as to establish fundamental constitutional rights and genuine political enfranchisement in FATA, along with a state apparatus capable of upholding the rule of law and bringing violent extremists to justice.

Islamabad/Washington/Brussels, 21 May 2013