KABUL, Afghanistan — Pakistan closed down a critical supply route for U.S. and allied forces in Afghanistan 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 that 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 believed to be especially unhappy, and there have been recent concerns about a possible coup.
Pakistan's formal protest, the second this week, was delivered to ISAF headquarters in Brussels.
"Incursions and strikes of this nature are not only unacceptable but could oblige Pakistan to consider response options," Pakistan said in the protest.
"Such incidents create serious misgivings and thus defeat the very basis of cooperation in pursuit of the common objective of combating terrorism," it said.
American officials sought to contain the damage from the incident and ensure the rapid reopening of the essential supply route.
Sen. John Kerry, D-Mass, spoke by phone with Pakistan Prime Minister Yousuf Raza Gilani and said he was assured that the attack would not create long-lasting problems for relations between the two countries.
ISAF officials said the closure had had no serious impact so far on the supply route and expressed confidence that the border crossing, which serves as an essential supply line for U.S.-led forces in Afghanistan, would quickly reopen.
However, Pakistan Interior Minister Rehman Malik said the government needed a full explanation.
"We will have to see whether we are allies or enemies," he told reporters.
While rare, Pakistan has used the closure of the border as a pressure point against the U.S. in the past.
Analysts and diplomats in Pakistan were puzzled about the sudden spate of "hot pursuit" by US forces that has again increased friction between the two countries.
In June 2008, a similar ISAF attack killed 11 Pakistani border troops, Three months later, U.S. commandos targeted a suspected insurgent compound in South Waziristan that killed 20. Pakistan officials said most of the dead were civilians.
Panetta's talks were believed to partly focus on a plot to attack multiple sites in Europe that was being reportedly hatched in Pakistan's tribal area, by individuals holding European passports. The revelation of the plot is said to be the reason behind the huge ramp up in drone strikes this month.
Also on Thursday, ISAF said that its forces had accidentally killed four Afghan civilians and injured three others while battling insurgents on Wednesday in eastern Afghanistan's Ghazni province.
ISAF said that its helicopters accidentally hit civilians while fighting eight insurgents.
"We deeply regret that our operation resulted in civilian loss of life and we express our sincerest condolences to the families," said Rear Adm. Greg Smith, the U.S.-led military's chief spokesman, who said the families would be compensated for their losses.
While tensions mounted on the border, ISAF said that five troops were killed in southern Afghanistan, bringing the military coalition death toll for September to 62, according to iCasualties, the website that tracks military deaths in Afghanistan and Iraq.
(Shah is a McClatchy special correspondent.)
MORE FROM MCCLATCHY
Follow Dion Nissenbaum on Twitter.