WASHINGTON — President Bush secretly approved orders in July that for the first time allow American Special Operations forces to carry out ground assaults inside Pakistan without the prior approval of the Pakistani government, according to senior American officials.

The classified orders signal a watershed for the Bush administration after nearly seven years of trying to work with Pakistan to combat the Taliban and Al Qaeda, and after months of high-level stalemate about how to challenge the militants’ increasingly secure base in Pakistan’s tribal areas.

American officials say that they will notify Pakistan when they conduct limited ground attacks like the Special Operations raid last Wednesday in a Pakistani village near the Afghanistan border, but that they will not ask for its permission.

“The situation in the tribal areas is not tolerable,” said a senior American official who, like others interviewed for this article, spoke on condition of anonymity because of the delicate nature of the missions. “We have to be more assertive. Orders have been issued.”

The new orders reflect concern about safe havens for Al Qaeda and the Taliban inside Pakistan, as well as an American view that Pakistan lacks the will and ability to combat militants. They also illustrate lingering distrust of the Pakistani military and intelligence agencies and a belief that some American operations had been compromised once Pakistanis were advised of the details.

The Central Intelligence Agency has for several years fired missiles at militants inside Pakistan from remotely piloted Predator aircraft. But the new orders for the military’s Special Operations forces relax firm restrictions on conducting raids on the soil of an important ally without its permission.

Pakistan’s top army officer said Wednesday that his forces would not tolerate American incursions like the one that took place last week and that the army would defend the country’s sovereignty “at all costs.”

It is unclear precisely what legal authorities the United States has invoked to conduct even limited ground raids in a friendly country. A second senior American official said that the Pakistani government had privately assented to the general concept of limited ground assaults by Special Operations forces against significant militant targets, but that it did not approve each mission.

The official did not say which members of the government gave their approval.

Any new ground operations in Pakistan raise the prospect of American forces being killed or captured in the restive tribal areas — and a propaganda coup for Al Qaeda. Last week’s raid also presents a major test for Pakistan’s new president, Asif Ali Zardari, who supports more aggressive action by his army against the militants but cannot risk being viewed as an American lap dog, as was his predecessor, Pervez Musharraf.

The new orders were issued after months of debate inside the Bush administration about whether to authorize a ground campaign inside Pakistan. The debate, first reported by The New York Times in late June, at times pitted some officials at the State Department against parts of the Pentagon that advocated aggressive action against Qaeda and Taliban targets inside the tribal areas.

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.”

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.”