The American official, speaking on condition of anonymity because of the sensitivity of cross border operations, told The Associated Press that the raid occurred on Pakistani soil about one mile from the Afghan border. The official didn't provide any other details.
Pakistan's Foreign Ministry launched a protest, saying U.S.-led troops flew in from Afghanistan for the attack on a village. An army spokesman warned that the apparent escalation from recent missile strikes on militant targets along the Afghan border would further anger Pakistanis and undercut cooperation in the war against terrorist groups.
The boldness of the thrust fed speculation about the intended target. But it was unclear whether any extremist leader was killed or captured in the operation, which occurred in one of the militant strongholds dotting a frontier region considered a likely hiding place for Osama bin Laden and al-Qaida's No. 2 leader, Ayman al-Zawahri.
U.S. military and civilian officials declined to respond to Pakistan's complaints. But one official, a South Asia expert who agreed to discuss the situation only if not quoted by name, suggested the target of any raid like that reported Wednesday would have to be extremely important to risk an almost assured "big backlash" from Pakistan.
"You have to consider that something like this will be a more-or-less once-off opportunity for which we will have to pay a price in terms of Pakistani cooperation," the official said.
Suspected U.S. missile attacks killed at least two al-Qaida commanders this year in the same region, drawing protests from Pakistan's government that its sovereignty was under attack. U.S. officials did not acknowledge any involvement in those attacks.
But American commanders have been complaining publicly that Pakistan puts too little pressure on militant groups that are blamed for mounting violence in Afghanistan, stirring speculation that U.S. forces might lash out across the frontier.
Circumstances surrounding Wednesday's raid weren't clear, but U.S. rules of engagement allow American troops to chase militants across the border into Pakistan's lawless tribal region when they are attacked. They may only go about six miles on the ground, under normal circumstances. U.S. rules allow aircraft to go 10 miles into Pakistan air space.
In other signs of Pakistan's precarious stability three days before legislators elect a successor to Pervez Musharraf as president, snipers shot at the prime minister's limousine near Islamabad and government troops killed two dozen militants in another area of the restive northwest.
Pakistani officials said they were lodging strong protests with the U.S. government and its military representative in Islamabad about Wednesday's raid in the South Waziristan area, a notorious hot bed of militant activity.
The Foreign Ministry called the strike "a gross violation of Pakistan's territory," saying it could "undermine the very basis of cooperation and may fuel the fire of hatred and violence that we are trying to extinguish."
Prior to the U.S. military confirming the U.S. raid, Pakistan government and military officials had insisted that either the NATO force or the U.S.-led coalition in Afghanistan -- both commanded by American generals -- were responsible.
The army's spokesman, Maj. Gen. Athar Abbas, said the attack was the first incursion onto Pakistani soil by troops from the foreign forces that ousted Afghanistan's hard-line Taliban regime after the Sept. 11 attack on the U.S.
He said the attack would undermine Pakistan's efforts to isolate Islamic extremists and could threaten NATO's major supply lines, which snake from Pakistan's Indian Ocean port of Karachi through the tribal region into Afghanistan.
"We cannot afford a huge uprising at the level of tribe," Abbas said. "That would be completely counterproductive and doesn't help the cause of fighting terrorism in the area."
A spokesman for NATO troops in Afghanistan denied any involvement in the raid.
The Pakistani anger threatens to upset efforts by American commanders to draw Pakistan's military into the U.S. strategy of dealing harshly with the militants.
Adm. Mike Mullen, chairman of the Joint Chiefs of Staff, met last week with Gen. Ashfaq Kayani, the Pakistani army chief. Mullen said he came away encouraged that Pakistanis were becoming more focused on the problem of militants using the country as a safe haven.
However, Abbas, the army spokesman, said Wednesday that cross-border commando operations were not discussed and he reiterated Pakistan's position that its forces should be exclusively responsible for operations on its territory.
Pakistani officials say the U.S. and NATO should share intelligence and allow Pakistani troops to execute any raids needed inside Pakistan. However, Washington has accused rogue elements in Pakistan's main intelligence service of leaking sensitive information to militants.
American officials say destroying militant sanctuaries in Pakistani tribal regions is key to defeating Taliban-led militants in Afghanistan whose insurgency has strengthened every year since the fundamentalist militia was ousted for harboring bin Laden.
But there has been debate in Washington over how far the U.S. can go on its own.
Citing witness and intelligence reports, Abbas said troops flew in on at least one big CH-47 Chinook transport helicopter, blasted their way into several houses and gunned down men they found there.
He said there was no evidence that any of those killed were insurgents or that the raiders abducted any militant leader, but he acknowledged Pakistan's military had no firsthand account.
There were differing reports on how many people were killed. The provincial governor claimed 20 civilians, including women and children, died. Army and intelligence officials, as well as residents, said 15 people were killed.
Habib Khan Wazir, an area resident, said he heard helicopters, then an exchange of gunfire.
"Later, I saw 15 bodies inside and outside two homes. They had been shot in the head," Wazir said by phone. He claimed all the dead were civilians.
Near Islamabad, meanwhile, snipers fired at a motorcade near the capital as it headed to the airport to pick up the prime minister, hitting the window of his car at least twice, officials said.
Neither Prime Minister Yousuf Raza Gilani nor his staff were in the vehicles.
Muslim Khan, a spokesman for the banned militant organization Tahrik-e-Taliban, claimed responsibility and pledged more attacks in retaliation for army operations in tribal areas and the Swat Valley along the border with Afghanistan.
In Washington, Secretary of State Condoleezza Rice declined to comment on the claimed cross-border raid, but she said the U.S. would continue to work with Gilani's government.
"I am relieved, of course, that the incident aimed at the Pakistani prime minister did not succeed," Rice said.
"We're going to be in continued contact with the Pakistanis as we both try to help them to build a strong economic foundation, to build a strong democratic foundation and to fight the terrorists who are a threat not just to the United States and to Afghanistan but to Pakistan as well."