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.
Toward that goal, Admiral Mullen said he had ordered a comprehensive military strategy to address the border region between Pakistan and Afghanistan.
The commando raid last week and an increasing number of recent missile strikes are part of a more aggressive overall American campaign in the border region aimed at intensifying attacks on Al Qaeda and the Taliban in the waning months of the Bush administration, with less than two months to go before November elections.
State Department officials, as well as some within the National Security Council, have expressed concern about any Special Operations missions that could be carried out without the approval of the American ambassador in Islamabad.
The months-long delay in approving ground missions created intense frustration inside the military’s Special Operations community, which believed that the Bush administration was holding back as the Qaeda safe haven inside Pakistan became more secure for militants.
The stepped-up campaign inside Pakistan comes at a time when American-Pakistani relations have been fraying, and when anger is increasing within American intelligence agencies about ties between Pakistan’s Inter-Services Intelligence Directorate, known as the ISI, and militants in the tribal areas.
Analysts at the C.I.A. and other American spy and security agencies believe not only that the bombing of India’s embassy in Kabul, Afghanistan, in July by militants was aided by ISI operatives, but also that the highest levels of Pakistan’s security apparatus — including the army chief, Gen. Ashfaq Parvez Kayani — had knowledge of the plot.
“It’s very difficult to imagine he was not aware,” a senior American official said of General Kayani.
American intelligence agencies have said that senior Pakistani national security officials favor the use of militant groups to preserve Pakistan’s influence in the region, as a hedge against India and Afghanistan.
In fact, some American intelligence analysts believe that ISI operatives did not mind when their role in the July bombing in Kabul became known. “They didn’t cover their tracks very well,” a senior Defense Department official said, “and I think the embassy bombing was the ISI drawing a line in the sand.” New York Times/posted by Bulatlat