Pakistani soldiers
© ReutersPakistani soldiers at Shamsi air base on Sunday, in a photograph provided by the Pakistani military’s public relations arm.
Islamabad, Pakistan - The Central Intelligence Agency has vacated an air base in western Pakistan that it had been using for drone strikes against militants in the country's tribal areas, the Pakistani military said on Sunday.

Pakistan had ordered the C.I.A. to leave the Shamsi air base in protest over NATO airstrikes that killed at least 25 Pakistani soldiers near the border with Afghanistan on Nov. 26. Pakistan has also blocked all NATO logistical supplies from crossing the border into Afghanistan since the clash.

Pentagon and Obama administration officials declined to comment publicly on the departure from the Shamsi air base.

But a senior American counterterrorism official, speaking on condition of anonymity because the drone operations at Shamsi were classified, said that vacating the base would not end American counterterrorism operations in Pakistan. "The United States retains robust capabilities to fight Al Qaeda and its militant allies," the official said. "Our operations will continue."

Pakistani officials have repeatedly accused NATO forces of deliberately attacking the Pakistani soldiers at two military check posts; American officials have said the airstrikes were an unfortunate accident.

In response to the attacks, Pakistan gave the C.I.A. 15 days to vacate the Shamsi base, which is about 200 miles southwest of the city of Quetta in Baluchistan Province. Inter Services Public Relations, the media wing of the Pakistani military, said the last flight carrying American personnel and equipment left the base on Sunday. "The base has been taken over by the army," the agency's statement said.

While United States officials do not comment publicly on drone operations against militants who plan attacks on Afghanistan from havens in the Pakistani tribal areas, operations had been reduced at the Shamsi air base since May, when a Navy Seal commando raid killed Osama bin Laden near Islamabad. The United States also carries out drone strikes from bases in Afghanistan.

After the Bin Laden raid, Pakistan insisted that the C.I.A. shut down its operations at the Shamsi base, but it later relented, permitting scaled-down operations.

The attacks on the Pakistani check points two weeks ago have stoked nationalist passions in the country, where anti-American sentiment was already running high. Angry demonstrations erupted after the airstrikes, and in an additional sign of protest, the Pakistani government decided not to attend an international conference on the future of Afghanistan held last week in Bonn, Germany.

Although American officials have expressed hope that their working relationship with the Pakistanis will not break down, Pakistani officials have insisted on rewriting the rules of bilateral cooperation.

Prime Minister Yousaf Raza Gilani said Sunday in an interview with the BBC that Pakistan might continue to block NATO supply convoys from entering Afghanistan for several more weeks.

"There is a credibility gap," Mr. Gilani told the BBC. "We are working together, and still we don't trust each other."

To build confidence, Mr. Gilani said, Pakistan is creating what he called "new rules of engagement with the United States."

"Then I think we should trust each other better," he said.