The Obama administration's aggressive drone program in Pakistan came under renewed attack this week, with Amnesty International suggesting that the United States is engaged in war crimes and visiting Prime Mininster Nawaz Sharif describing the strikes as a "major irritant" in relations.
But what is obscured by the public dispute is that there has been, since the administrations of George W. Bush and Pervez Musharraf, a secret agreement in place by which Pakistani military and intelligence authorities have approved many of the strikes, U.S. and Pakistani officials say.
"The exact terms were never shared with civilians but there was a protocol between the Musharraf government and the Americans," says a former senior Pakistani official who would discuss the classified matter only on condition of anonymity. "When the civilian government came in [in 2008], it was informed about it but there was no renegotiation."
Even so, this official said that civilian leaders in Islamabad have made sporadic efforts to renegotiate. "Both [former President Asif Ali] and Sharif have approached Washington to say, 'Can we talk about it?'"
Sharif said he brought up the issue of drones in his White House meeting with President Obama on Wednesday, "emphasizing the need for an end to such strikes." The Washington Post also reported late Wednesday that it had obtained top-secret CIA documents and Pakistani diplomatic memos detailing deep cooperation between the United States and Pakistan on drone targeting.
Because the details are not publicly known, it is not clear to what extent the Pakistani military and intelligence apparatus gained approval authority for all drone strikes. In his new book, "Magnificent Delusions: Pakistan, the United States and an Epic History of Misunderstanding," former Pakistani ambassador to Washington Husain Haqqani writes that the Pakistani ISI actually resisted U.S. efforts to keep its own government in Islamabad informed. "The CIA and the ISI [Pakistani intelligence] communicated regularly on the strikes," Haqqani says. "The ISI did not like Pakistani civilian officials finding out anything about their dealings with the United States about armed Predator drones, but the U.S. government wanted the civilian leadership to remain in the picture." The ISI, Haqqani added, was in the habit of "protesting against the drones publicly while privately negotiating over whom the drones would target."
But the two governments increasingly diverged over the nature of the enemy, with the ISI wanting to protect some of its jihadist allies in the struggle for influence with India and inside Afghanistan, and to target only certain al Qaida-linked groups. Trust between the two sides was badly damaged after the U.S. unilaterally targeted Osama bin Laden in a strike by Navy SEALs in Abbottabad in May 2011, completely surprising Pakistani military and intelligence officials.
Officials say that a major reason why the Obama administration resisted efforts by Congress to obtain the full range of its classified legal memos justifying so-called targeted killing was to protect the secret protocols with Pakistan and other countries, such as Yemen.
Last February, a legal expert outside the government who is intimately familiar with the contents of the memos drafted by the Justice Department's Office of Legal Counsel said that the government-to-government accords on the conduct of drone strikes were a key element not contained in a Justice Department "white paper" revealed by NBC News. He said it was largely in order to protect this information that the targeted-killing memos drafted by Justice's Office of Legal Counsel were even withheld from congressional committees. "That is what is missing from the white paper but forms a core part of the memos," the expert said.