WASHINGTON -- In the skies above Yemen, the Pentagon's armed drones have stopped flying, a result of the ban on U.S. military drone strikes imposed by the government there after a number of botched operations in recent years killed Yemeni civilians. But the CIA's drone war in Yemen continues.
In Pakistan, the CIA remains in charge of drone operations, and may continue to be long after U.S. troops have left Afghanistan.
And in Jordan, it is the CIA 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 Brennan, the CIA'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, 2001, attacks toward more traditional roles carrying out espionage, intelligence collection and analysis. And in a speech last May in which he sought to redefine U.S. policy toward terrorism, President Barack 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 CIA.
"Some might want to get the CIA out of the killing business, but that's not happening anytime soon," said Michael Sheehan, who until last year was the Secretary of senior Pentagon official in charge of special operations and now holds a 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 also facing a reckoning for other aspects of the CIA'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 CIA history Mr. Brennan has publicly disavowed. The U.S. Justice Department has been drawn into a dispute between the agency and the committee, and is looking into a charge by Sen. 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 CIA 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.
Now, Mr. Brennan is in charge of a counterterrorism apparatus that has steadily grown in budget, manpower and influence for more than a decade. While officials said Mr. Brennan has pushed for more resources to counter traditional adversaries like Russia and China, as well as newer threats like cyberwarfare, the agency's Counterterrorism Center, known as the CTC, remains a powerful force both inside the agency and on Capitol Hill.
"I think that most of the CIA is behind the changes, but the CTC community has grown dramatically since 9/11 and is fighting to keep its turf," Mr. Sheehan said. "And, they've been somewhat successful in that regard, especially with the drone programs."
Influential lawmakers from both parties have fought to protect the CIA's role in the drone wars and prevent the proposed shift of the bulk of drone operations to the Pentagon.
Both Ms. Feinstein and Rep. Mike Rogers of Michigan, chairman of the House Intelligence Committee, have urged Mr. Brennan to push back against the White House policy announced last May, citing what they regard as the Pentagon's poor performance in lethal operations outside of Iraq and Afghanistan.
A number of bungled drone strikes carried out by the Joint Special Operations Command in Yemen led the government there in recent months to temporarily ban drone strikes by the military, which are launched from a U.S. base in Djibouti.
Officials said that the ban, not previously reported, came after a military drone strike in December killed a number of civilians who were part of a wedding procession in a desolate region south of Yemen's capital, Sanaa.
Meanwhile, the CIA continues to wage its own drone war in Yemen, launching the unmanned planes from Saudi Arabia.
In Pakistan, where the CIA also is in charge of the drone program, the pace of strikes has declined sharply, and there have been none since the government in Islamabad formally entered peace talks with the Pakistani Taliban, according to the Bureau of Investigative Journalism, a group that tracks drone strikes.
But U.S. officials said that the drone program there could continue for years, and Pakistan's government has long insisted that it be run by the CIA, not the U.S. military.
A White House spokeswoman said there had been "no change in policy" since Mr. Obama's speech last May announcing changes to targeted killing policy.
"The plan is to transition to these standards and procedures over time, in a careful, coordinated and deliberate manner," said Caitlin Hayden, the spokeswoman. "I'm not going to speculate on how long the transition will take, but we're going to ensure that it's done right and not rushed."