Details about last week’s commando operation have emerged that indicate the mission was more intrusive than had previously been known.

According to two American officials briefed on the raid, it involved more than two dozen members of the Navy Seals who spent several hours on the ground and killed about two dozen suspected Qaeda fighters in what now appeared to have been a planned attack against militants who had been conducting attacks against an American forward operating base across the border in Afghanistan.

Supported by an AC-130 gunship, the Special Operations forces were whisked away by helicopters after completing the mission.

Although the senior American official who provided the most detailed description of the new presidential order would discuss it only on condition of anonymity, his account was corroborated by three other senior American officials from several government agencies, all of whom made clear that they supported the more aggressive approach.

Pakistan’s government has asserted that last week’s raid achieved little except killing civilians and stoking anti-Americanism in the tribal areas.

“Unilateral action by the American forces does not help the war against terror because it only enrages public opinion,” said Husain Haqqani, Pakistan’s ambassador to Washington, during a speech on Friday. “In this particular incident, nothing was gained by the action of the troops.”

As an alternative to American ground operations, some Pakistani officials have made clear that they prefer the C.I.A.’s Predator aircraft, operating from the skies, as a method of killing Qaeda operatives. The C.I.A. for the most part has coordinated with Pakistan’s government before and after it has launched missiles from the drone. On Monday, a Predator strike in North Waziristan killed several Arab Qaeda operatives.

A new American command structure was put in place this year to better coordinate missions by the C.I.A. and members of the Pentagon’s Joint Special Operations Command, made up of the Army’s Delta Force and the Navy Seals.

The move was intended to address frustration on the ground about different agencies operating under different marching orders. Under the arrangement, a senior C.I.A. official based at Bagram air base in Afghanistan was put in charge of coordinating C.I.A. and military activities in the border region.

Spokesmen for the White House, the Defense Department and the C.I.A. declined to comment on Wednesday about the new orders. Some senior Congressional officials have received briefings on the new authorities. A spokeswoman for Senator Carl Levin, a Michigan Democrat who leads the Armed Services Committee, declined to comment.

American commanders in Afghanistan have complained bitterly that militants use sanctuaries in Pakistan to attack American troops in Afghanistan.

“I’m not convinced we’re winning it in Afghanistan,” Adm. Mike Mullen, the chairman of the Joint Chiefs of Staff, told the House Armed Services Committee on Wednesday. “I am convinced we can.”
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