U.S. officials say that the CIA’s massive stations in Kabul and Baghdad will likely remain the agency’s largest overseas outposts for years, even after U.S. military forces leave. (Alex Wong/Getty Images)

The CIA is expected to maintain a large clandestine presence in Iraq and Afghanistan long after the departure of conventional U.S. troops as part of a plan by the Obama administration to rely on a combination of spies and Special Operations forces to protect U.S. interests in the two longtime war zones, U.S. officials said.

U.S. officials said that the CIA’s stations in Kabul and Baghdad will probably remain the agency’s largest overseas outposts for years, even if they shrink from record staffing levels set at the height of American efforts in those nations to fend off insurgencies and install capable governments.

The withdrawal of U.S. forces from Iraq in December has moved the CIA’s emphasis there toward more traditional espionage — monitoring developments in the increasingly antagonistic government, seeking to suppress al-Qaeda’s affiliate in the country and countering the influence of Iran.

In Afghanistan, the CIA is expected to have a more aggressively operational role. U.S. officials said the agency’s paramilitary capabilities are seen as tools for keeping the Taliban off balance, protecting the government in Kabul and preserving access to Afghan airstrips that enable armed CIA drones to hunt al-Qaeda remnants in Pakistan.

As President Obama seeks to end a decade of large-scale conflict, the emerging assignments for the CIA suggest it will play a significant part in the administration’s search for ways to exert U.S. power in more streamlined and surgical ways.

As a result, the CIA station in Kabul — which at one point had responsibility for as many as 1,000 agency employees in Afghanistan — is expected to expand its collaboration with Special Operations forces when the drawdown of conventional troops begins.

Navy Adm. William McRaven, the Special Operations commander who directed the raid that killed Osama bin Laden last year, signaled the transition during remarks Tuesday in Washington. “I have no doubt that Special Operations will be the last to leave Afghanistan,” McRaven said.

The CIA declined to comment. But current and former intelligence officials quibbled with the accuracy of McRaven’s assertion.

“I would say the agency will be the last to leave,” said a CIA veteran with extensive experience in Afghanistan and Pakistan. “We were the first to get there” after the Sept. 11, 2001, attacks, the former official said.

Force size evolving

U.S. officials said the size of the agency’s presence in Afghanistan over the next several years has not been determined, and the CIA’s assignment is likely to be adjusted as the administration’s troop withdrawal plans evolve.

In some scenarios, teams of CIA and Special Operations troops could divide territory and lists of Taliban targets with Afghan forces, although officials said there will probably be extensive collaboration and overlap.

CIA paramilitary operatives were the first U.S. personnel to enter Afghanistan after the Sept. 11 attacks, linking up with Northern Alliance fighters weeks before U.S. military commandos arrived. More than a decade later, the CIA still has extensive paramilitary assets there.

“Like Special Forces, the intelligence community is used to doing a lot with a small footprint, using its agility to address a host of national security concerns,” said a U.S. official, speaking on the condition of anonymity to discuss intelligence matters.

The agency controls counterterrorism pursuit teams made up of dozens of Afghan fighters funded and trained by the CIA. The CIA has largely bankrolled and built the Afghan intelligence service. And the agency maintains a constellation of bases along the border with Pakistan.

Some of those sites are likely to be closed, current and former officials said. The 2010 death of seven CIA employees and contractors in a suicide bombing by a double agent at a CIA base in Khost province underscored the vulnerability of such remote outposts. As conventional forces depart, officials said, the agency will probably concentrate more of its remaining employees at compounds in Kabul and at the Bagram air base north of the capital.

As a result, more territory may be ceded to the Taliban. “We can lose the countryside, but I don’t think we’re going to lose Kabul and Bagram,” said the former senior CIA officer, who added that the agency could end up adding paramilitary personnel in Afghanistan as the size of the U.S. military deployment shrinks.

The Obama administration has said it plans to pull about 22,000 troops out of Afghanistan by September, reducing the overall U.S. force to 68,000. Defense Secretary Leon E. Panetta fanned speculation that the drawdown could be accelerated by saying last week that the United States hoped to end its combat mission in Afghanistan by mid-2013.

If the agency is tapped to play an expanded role in Afghanistan and Iraq, the landscape will be familiar to many across the CIA’s senior ranks. Retired Army Gen. David H. Petraeus commanded U.S. forces in both countries before taking over as director of the CIA. A senior CIA operative who twice served as station chief in Kabul now heads the agency’s Special Activities Division, its paramilitary branch.

Scaling back spending

The pressure to maintain a sizable presence in Kabul and Baghdad comes as the CIA and other intelligence agencies face spending cuts for the first time since their budgets began expanding after the Sept. 11 attacks.

The CIA’s annual budget is believed to be about $5.5 billion. In congressional testimony last week, Director of National Intelligence James R. Clapper said, “We’re not going to do more with less and all these other cliches. . . . We will just simply have less capability.”

At their peak, the CIA’s stations in Kabul and Baghdad were the largest and second-largest in agency history, surpassing the size of the CIA’s station in Saigon at the height of the Vietnam War. CIA veterans stressed that those totals included more security, support and analytic personnel than clandestine operatives.

At the high point of the U.S. military surge in Iraq, the CIA had as many as 700 employees in the country. Most worked in Baghdad’s Green Zone, but hundreds were also scattered across safe houses in population centers and regional U.S. military outposts.

The departure of U.S. forces in December has forced the agency to shutter many of those facilities, according to former CIA officials who said the agency’s presence has probably been reduced by half.

“We had bases all over the country, but that’s not the case anymore,” said a second former CIA officer who served in Iraq. The development is likely to hamper intelligence collection, the former officer said. “You can’t put hundreds of people in the embassy and expect that to be your platform in Iraq.”

Staff writer Julie Tate contributed to this report.