But even those who agree with the decision said it may prove more difficult for Obama to dismantle the CIA’s drone program than it was to shutter its secret prisons, because of the agency’s expertise as well as circumstances that at times enable the CIA to operate in places off-limits to the Defense Department.

“You have to go into this with some concern,” a former senior U.S. counter­terrorism official said of the plan. “It didn’t work before. Will it work this time?”…

In an interview in late 2010, a senior Obama administration official stressed that the CIA was running the drone campaign in Pakistan mainly because the agency was first to develop the technology after the Sept. 11, 2001, terrorist attacks and because Pakistan’s government insisted on secrecy so that it could deny any U.S. operations on its soil.

“It has been in Yemen a different story, a different history, a different evolution,” the official said, making clear that the administration regarded the CIA campaign as an anomaly and saw lethal operations as the province of the military.

The U.S. military’s elite Joint Special Operations Command was already flying drones over Yemen from a base in Djibouti on the Horn of Africa. Using drones, warships and conventional aircraft, JSOC had already launched a flurry of strikes against al-Qaeda targets.