As part of a bureaucratic reshuffling last month by John O. Brennan, the C.I.A. director, Mr. D’Andrea has been replaced as head of the drone program by Chris Wood. After the Sept. 11, 2001, attacks, Mr. Wood held leadership roles in Alec Station, the group that led the hunt for Qaeda suspects and was central to the interrogation program. He ultimately was in charge of that unit and would later serve as station chief in Kabul. Most recently, he supervised all operations in Afghanistan and Pakistan. Mr. Wood now runs a targeted killing program that is the subject of multiple investigations that Mr. Obama announced last week.

And yet the president has given no indication that he intends to shut down the drone program, and both he and his aides continue to praise it as a method of warfare that offers the White House an alternative to messy wars of occupation like in Iraq and Afghanistan. A leitmotif of Mr. Obama’s re-election campaign in 2012 was his administration’s success in killing high-ranking Qaeda operatives in Pakistan — even if it was never mentioned that the C.I.A. was doing the killing.

Image John O. Brennan, the C.I.A. director, has been slow to dial back paramilitary operations. Credit... Justin Lane/European Pressphoto Agency

Despite the drone program reforms that Mr. Obama announced in May 2013, White House officials have shown little enthusiasm for ensuring that many of them are adopted. It is the C.I.A., not the Pentagon, that continues to carry out of all of the drone strikes in Pakistan and most of those in Yemen. An internal administration proposal to create a counterterrorism center at the Pentagon, modeled after the C.I.A. unit that runs the drone strikes, was quietly scrapped.

When Mr. Brennan, a former top White House counterterrorism adviser who remains close to Mr. Obama, became C.I.A. director in late 2013, he announced an intention to dial back the paramilitary operations that have transformed the agency since the Sept. 11 attacks. His goal, he said during his confirmation hearings, was to refocus the agency on the traditional work of intelligence collection and espionage that had sometimes been neglected.

But that effort too is slow going, and Mr. Brennan has not pushed forcefully for moving drone operations away from the C.I.A., something he advocated when he was in the White House during Mr. Obama’s first term. In a sign of the continued prominence of military operations inside the agency, Mr. Brennan recently named Greg Vogel, a former agency paramilitary officer, to take over the C.I.A.’s vaunted Directorate of Operations. That position has traditionally gone to C.I.A. officers who ascended the ranks because of their success in traditional espionage work.

Mr. Vogel, identified in news accounts as “Spider” and in a memoir by the former C.I.A. Director George J. Tenet as “Greg V.,” was one of the first C.I.A. officers to enter Afghanistan when the war began in 2001. He was credited during that time with saving the life of Hamid Karzai, the future Afghan president, during a bomb strike. He later served as the C.I.A. station chief in Kabul and eventually became the head of the agency’s Special Activities Division, which runs many paramilitary operations.