WASHINGTON (CNN) -- President Bush authorized U.S. special forces to conduct ground assaults inside Pakistan without seeking Islamabad's permission first, a senior American intelligence official said Thursday.

Adm. Mike Mullen, chairman of the Joint Chiefs, said better U.S.-Pakistan cooperation is needed to fight terror.

"We have had the president's OK for months," said the official, who declined to be identified because the order is classified. "It is my understanding that the Pakistanis are well aware of the change."

The official would not elaborate on the exact nature of the order.

The official said Pakistan's leaders will be notified during an assault or after the fact, depending on the situation but "most definitely after a decision has been made and things set in motion."

National Security Council spokesman Gordon Johndroe declined to comment on the report.

Pakistan's ambassador to the United States said he had been "assured at the highest level by the U.S. government that no such orders exist," and that Pakistan would be very displeased if they did.

"We will not allow foreign troops on Pakistani soil under any condition," Ambassador Husain Haqqani said.

The United States is concerned that Taliban and al Qaeda forces operate with relative impunity in tribal areas along Pakistan's border with Afghanistan, and use those areas as a staging ground to attack U.S. forces and their allies inside Afghanistan.

The intelligence official's revelation comes after what Pakistan said was a September 3 incursion by U.S. forces into the country. A senior U.S. official said last week that U.S. helicopters dropped troops in the village of Angoor Adda in South Waziristan, which borders Afghanistan. Watch a report on new rules of engagement for hunting terrorists »

Local media reports said the troops came out of a chopper and fired on civilians. The U.S. official who spoke about the operation said a small number of women and children may have been in the immediate vicinity, but when the mission began, "everybody came out firing" from the compound.

Pakistan summoned the U.S. ambassador in Islamabad to complain about the incident, which it said killed 15 civilians. It called the raid "reckless."

Haqqani on Thursday insisted Pakistan would handle security within its borders.

"We have been assured that the United States ... fully understands that the most effective means of fighting terrorism would be to allow Pakistani military forces to operate on the Pakistani side, while letting international forces and Afghan forces operate on the Afghan side," he said.

Haqqani said unauthorized U.S. operations inside Pakistan would only harm relations between the two countries and added that the September 3 incursion was counterproductive.

"The kind of operation that we saw on the third of September is certainly not acceptable to the Pakistani people or the Pakistani government, and it does not advance the cause of the war against terror. It enrages the people of Pakistan," he said.

On Wednesday, Pakistan's top general, reacting to the September 3 operation, also said no foreign forces would be allowed to conduct operations there.

Pakistan's "territorial integrity ... will be defended at all cost and no external force is allowed to conduct operations ... inside Pakistan," according to a military statement attributed to Chief of Army Staff Gen. Parvez Kayani, who succeeded Pervez Musharraf after he stepped down as Pakistan's army chief last year.

Adm. Mike Mullen, chairman of the Joint Chiefs of Staff, said Wednesday that the United States and Pakistan must increase cooperation to battle al Qaeda and Taliban militants that are using areas along Pakistan's border with Afghanistan as a safe haven.

Mullen stressed that Afghanistan can't be referenced without "speaking of Pakistan," where, he said, the militant groups collaborate and communicate better, launch more sophisticated attacks, employ foreign fighters and use civilians as human shields. Watch how Pakistan is trying to fight militants »

"In my view, these two nations are inextricably linked in a common insurgency that crosses the border between them," he said, adding that he plans "to commission a new, more comprehensive strategy for the region, one that covers both sides of the border."

CNN's Nic Robertson, Barbara Starr and Brianna Keilar contributed to this report.

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