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.

A Human Rights Watch report this week also criticized the U.S. drone program in Yemen, saying the targeted airstrikes against alleged terrorists have violated international law by killing innocent civilians. But a year ago, the new leader of Yemen – another country with which Washington has signed a secret protocol on drones – publicly endorsed America's use of drones within his borders. "They pinpoint the target and have zero margin of error, if you know what target you're aiming at," the new Yemeni president, Abdu Rabbu Mansour Hadi, said at the Woodrow Wilson Center in Washington.