Al-Qaeda in the Arabian Peninsula chief Nasser al-Wuhayshi is pictured in the militant stronghold town of Jaar, Yemen, on April 28, 2012. (AFP/Getty Images)

The CIA did not know in advance that al-Qaeda’s leader in Yemen was among the suspected militants targeted in a lethal drone strike last week, according to U.S. officials who said that the operation went forward under counter­terrorism guidelines that were eased by the Obama administration after the collapse of the U.S.-backed government in Yemen this year.

The officials said that Nasir ­al-Wuhayshi, who also served as ­al-Qaeda’s overall second-in-command, was killed in a “signature strike,” in which the CIA is permitted to fire based on patterns of suspected militant activity even if the agency does not know the identities of those who could be killed.

The disclosure indicates that the CIA continues to employ a controversial targeting method that the administration had signaled in 2013 that it intended to phase out, particularly in Yemen, which U.S. officials have said is subject to more stringent rules on the use of lethal force than in Pakistan.

The reliance on signature strikes would help explain an increase in the pace of drone operations in Yemen over the past six months. U.S. officials said this week that the campaign has ­inflicted major damage on al-Qaeda’s franchise in that country even after joint U.S.-Yemen counter­terrorism operations on the ground were effectively suspended several months ago.

The CIA and the U.S. Joint Special Operations Command have carried out at least a dozen strikes in Yemen since January, a number approaching the total for 2014, according to data compiled by the New America Foundation.

Al-Qaeda’s branch in Yemen says its leader, Nasir al-Wuhayshi, has been killed in a U.S. drone strike. (Reuters)

Human rights groups have been sharply critical of the use of signature strikes. Jameel Jaffer, a senior lawyer at the ACLU involved in lawsuits aimed at forcing the administration to disclose details of its counter­terrorism policies, said that the use of such strikes would cast significant doubt on the administration’s assertions about restraints imposed on the use of lethal force.

“If government is carrying out signature strikes in Yemen, the administration needs to explain whether, to what extent, and on which agencies these restraints have actually been imposed,” Jaffer said in an e-mail Wednesday. “So many of the government’s assertions about its policies have turned out to be incomplete, misleading, or even false.”

The CIA declined to comment on the killing of Wuhayshi or any aspect of the agency’s drone operations in Yemen. But U.S. officials insisted that there was never a comprehensive ban on the use of signature strikes in that country and stressed that other aspects of the White House guidelines — including a requirement of “near certainty” that no civilians will be harmed — remain in tact.

The White House did not respond to questions about the specific circumstances of the Wuhayshi killing or what current and former officials said were changes­ in lethal targeting guidelines. National Security Council spokesman Edward Price said that procedures announced in May 2013 “continue to apply in Yemen.”

A U.S. intelligence official attributed the killing of Wuhayshi and other al-Qaeda operatives in recent months to “the cumulative knowledge we have developed” of terrorist networks in the country, as well as adjustments seen necessary to “overcoming significant challenges and an evolving extremist landscape.”

That language referred in part to the defeat of a U.S.-backed government in Yemen that had cooperated extensively in counter­terrorism operations against al-Qaeda. U.S. officials said the stepped-up use of signature strikes is part of a broader easing of constraints on the CIA and U.S. military drone campaigns there to help compensate for the loss of a critical ally.

U.S. officials declined to discuss those changes­ in detail except to say there has been an effort to streamline an approval process that has required the CIA and U.S. military to obtain permission from President Obama or top White House officials before launching missiles from their fleets of armed drones.

The adjustments reflect the extent to which the proliferation of terrorist groups and political turbulence in the Middle East have complicated the administration’s efforts to adhere to policies it spent years developing to serve as a counter­terrorism “playbook.”

“If they got Wuhayshi this way, it’s going to embolden those who are in favor of more signature strikes,” said a former senior U.S. counter­terrorism official who served in the administration. “They would be fully justified in thinking that they’re in a far different universe than they thought they were entering in 2012,” when the playbook was being completed.

The years since then have seen the emergence of potent new groups, including the Islamic State, which has beheaded Western captives and seized territory in Iraq and Syria.

When those White House guidelines were unveiled in 2013, senior administration officials said one of the goals was to “narrow,” if not eliminate, the use of signature strikes in Yemen. They said the method would mainly remain in use in Pakistan, where CIA drones were used to pursue al-Qaeda as well as disrupt militants seen as posing threats to U.S. forces in Afghanistan.

The CIA’s use of signature strikes came under intense new criticism two months ago when it was disclosed that a January drone attack in Pakistan had killed two kidnapped Western aid workers, including a U.S. citizen, in a signature strike on an al-Qaeda compound.

U.S. officials said that the agency had the site under surveillance for hundreds of hours before the attack and that analysts were confident no civilians were in danger. The CIA learned only afterward that Warren Weinstein of Rockville, Md., and Giovanni Lo Porto of Italy were killed when more bodies were removed from the rubble than the agency had counted beforehand.

Obama subsequently apologized to their families and said the operation had been “fully consistent with the guidelines” established by his administration. But he also pledged “a full review of what happened,” language that some interpreted as a signal the White House might reconsider its willingness to allow lethal operations without knowing targets’ identities.

The Joint Special Operations Command’s drone program has also been plagued by problems. The elite command was forced to suspend lethal drone operations in Yemen after a 2013 strike killed at least a dozen civilians in a wedding convoy, although the JSOC has since been allowed to resume drone strikes there.

CIA officials have staunchly defended the targeting approach, saying that analysts poring over drone footage and other surveillance have become adept at detecting patterns — such as the composition and movement of a security detail — associated with senior al-Qaeda operatives.

U.S. officials have credited the method in accounting for many of the high-value al-Qaeda targets killed in Pakistan during a dramatic escalation in the drone campaign there during Obama’s first term.

A former senior U.S. official said that there were high-level discussions about whether to expand authority for signature strikes in Yemen, especially as al-Qaeda’s franchise there, al-Qaeda in the Arabian Peninsula, began to eclipse the parent organization as a perceived threat.

Obama at first resisted those proposals, scolding subordinates that the United States was not at war in Yemen. As AQAP expanded, Obama later endorsed a modified version of the targeting approach, one for which administration officials coined a term: terrorist attack disruption strikes, or TADS.

The publicly disclosed version of the administration’s counter­terrorism policy makes no explicit mention of signature strikes or TADS but includes a requirement of “near certainty that the terrorist target is present.”

A senior U.S. official said that the CIA does not use either the signature strike or TADS terminology. Instead, the official said, the agency describes drone attacks as either “HVT or non-HVT,” depending on whether a high-value target is in its sights.

Karen DeYoung and Julie Tate contributed to this report.