KABUL -- Pakistan closed down a critical supply route for U.S. and allied forces in Afghanistan on Thursday after U.S. helicopters crossed into Pakistan during a confused, predawn attack that killed three Pakistani paramilitary troops.

Pakistan shuttered one of the two main crossings into Afghanistan hours after a pair of Apache helicopters apparently attacked a border post, manned by the paramilitary Frontier Corps, about 200 yards inside Pakistan.

U.S. military officials said that the helicopters opened fire in self-defense after taking small-arms fire from unknown forces inside Pakistan.

Hundreds of supply trucks bound for the busy Torkham crossing north of Peshawar were sidelined in Pakistan as the U.S.-led International Security Assistance Force said it was investigating.

The incident immediately raised tensions between the uneasy allies even as CIA chief Leon Panetta was conferring with Pakistan President Asif Ali Zardari.

"The government of Pakistan strongly disapproves any incident of violation of its sovereignty," Zardari told the CIA chief, according to a statement from the president's office. "Any violation of internationally agreed principles is counter-productive and unacceptable."

Without directly accepting responsibility for killing the Frontiers Corps forces, ISAF issued a statement conveying "sincere condolences to the Pakistani military and the families of those who were killed or injured."

It was the second such helicopter incursion in five days. The first, last Saturday, drew an angry Pakistani response earlier this week.

According to the Pakistan military, the latest incident occurred at 5:25 a.m. Thursday, when two ISAF helicopters attacked the border post with rockets after Frontier Corps troops fired "warning shots" to let the aircraft know they had crossed into upper Kurram Agency in Pakistan's tribal area.

ISAF acknowledged that two Apache helicopters "briefly" crossed into Pakistani airspace.

"After the initial strike, the aircraft received what the crews assessed as effective small-arms fire from individuals just across the border in Pakistan," ISAF said. "Operating in self defense, the ... aircraft entered into Pakistani airspace killing several armed individuals."

Within hours, Pakistan closed the vital ISAF supply line that runs from Karachi, Pakistan, through the fabled Khyber Pass to the Torkham crossing. About half of ISAF supplies come through Torkham and the southern Spin Boldak crossing, according to the U.S. Central Command.

Pakistan's action appeared to be intended in part for domestic political consumption. The deeply unpopular U.S.-backed civilian government has come under wide criticism for its inept response to the country's devastating floods.

The army, which has ruled Pakistan for more than half its history, is thought to be especially unhappy, and there have been recent concerns about a possible coup.