WASHINGTON — In the skies above Yemen, the Pentagon’s armed drones have stopped flying, a result of the ban on American military drone strikes imposed by the government there after a number of botched operations in recent years killed Yemeni civilians. But the Central Intelligence Agency’s drone war in Yemen continues.
In Pakistan, the C.I.A. remains in charge of drone operations, and may continue to be long after American troops have left Afghanistan.
And in Jordan, it is the C.I.A. rather than the Pentagon that is running a program to arm and train Syrian rebels — a concession to the Jordanian government, which will not allow an overt military presence in the country.
Just over a year ago John O. Brennan, the C.I.A.’s newly nominated director, said at his confirmation hearing that it was time to refocus an agency that had become largely a paramilitary organization after the Sept. 11 attacks toward more traditional roles carrying out espionage, intelligence collection and analysis. And in a speech last May in which he sought to redefine American policy toward terrorism, President Obama expanded on that theme, announcing new procedures for drone operations, which White House officials said would gradually become the responsibility of the Pentagon.
But change has come slowly to the C.I.A.
“Some might want to get the C.I.A. out of the killing business, but that’s not happening anytime soon,” said Michael A. Sheehan, who until last year was the senior Pentagon official in charge of special operations and now holds the distinguished chair at West Point’s Combating Terrorism Center.
A number of factors — including bureaucratic turf fights, congressional pressure and the demands of foreign governments — have contributed to this delay. At the same time, Mr. Brennan is facing a reckoning for other aspects of the C.I.A.’s role at the forefront of the secret wars the United States has waged since 2001.
The declassification of a scathing report by the Senate Intelligence Committee about the agency’s detention and interrogation program will once again cast a harsh light on a period of C.I.A. history Mr. Brennan has publicly disavowed. The Justice Department has been drawn into a dispute between the agency and the committee, and is looking into a charge by Senator Dianne Feinstein, the committee’s chairwoman, that the agency broke the law by monitoring computers of committee staff working on the report.
Before taking charge of the C.I.A. last March, Mr. Brennan had spent four years as Mr. Obama’s top counterterrorism adviser, a job that put him in charge of the targeted killing operations that became a signature of the Obama administration’s approach to terrorism. It also made Mr. Brennan — who before working for Mr. Obama had spent 25 years at the C.I.A. — a powerful influence on a president with no experience in intelligence.
American officials said that in that role Mr. Brennan repeatedly cautioned Mr. Obama that the C.I.A.’s counterterrorism mission threatened to attenuate the agency’s other activities, most notably those of penetrating foreign governments and analyzing global trends. During his confirmation hearings, Mr. Brennan obliquely criticized the performance of American spy agencies in providing intelligence and analysis of the Arab revolutions that began in 2009, and said the C.I.A. needed to cede some of its paramilitary role to the Pentagon.
“The C.I.A. should not be doing traditional military activities and operations,” he said.