A full investigation will be conducted into a NATO attack that allegedly killed at least two dozen Pakistani troops, the Obama administration said Saturday.

In a joint statement on Saturday night, U.S. Secretary of State Hillary Rodham Clinton and Defence Secretary Leon Panetta said they had each spoken with their Pakistani counterparts to express their condolences for the loss of life.

The incident was a major blow to American efforts to rebuild an already tattered alliance vital to winding down the 10-year-old Afghan war. Islamabad called the bloodshed in one of its tribal areas a "grave infringement" of the country's sovereignty.

The announcement in Washington came after Pakistan said it would block vital supply routes for U.S.-led troops in Afghanistan and demanded Washington vacate a base used by American drones after coalition aircraft allegedly attacked two posts along a mountainous frontier that serves as a safe haven for militants.

A NATO spokesman said it was likely that coalition airstrikes caused Pakistani casualties, but an investigation was being conducted to determine the details. If confirmed, it would be the deadliest friendly fire incident by NATO against Pakistani troops since the Afghan war began a decade ago.

A prolonged closure of Pakistan's two Afghan border crossings to NATO supplies could cause serious problems for the coalition. The U.S., which is the largest member of the NATO force in Afghanistan, ships more than 30 per cent of its non-lethal supplies through Pakistan. The coalition has alternative routes through Central Asia into northern Afghanistan, but they are costlier and less efficient.

Last year, Pakistan temporarily closed one of its Afghan crossings to NATO supplies after U.S. helicopters accidentally killed two Pakistani soldiers. Suspected militants took advantage of the impasse to launch attacks against stranded or rerouted trucks carrying NATO supplies. The government reopened the border after about 10 days when the U.S. apologized. NATO said at the time the relatively short closure did not significantly affect its ability to keep its troops supplied.

But the reported casualties are much greater this time, and the relationship between Pakistan and the U.S. has severely deteriorated over the last year, especially following the covert American raid that killed Osama bin Laden in a Pakistani garrison town in May. Islamabad was outraged it wasn't told about the operation beforehand.

The government announced it closed its border crossings to NATO in a statement issued after an emergency meeting of the cabinet's defence committee chaired by Pakistani Prime Minister Yousuf Raza Gilani.

Pakistani security personnel stop trucks carrying supplies for NATO forces in the Pakistani tribal area of Khyber on Saturday. Muhammad Sajjad/Associated Press

It also said that within 15 days the U.S. must vacate Shamsi Air Base, which is located in southwestern Baluchistan province. The U.S. uses the base to service drones that target al-Qaeda and Taliban militants in Pakistan's tribal region when they cannot return to their bases inside Afghanistan because of weather conditions or mechanical difficulty, said U.S. and Pakistani officials, speaking on condition of anonymity to discuss sensitive strategic matters.

The government also plans to review all diplomatic, military and intelligence co-operation with the U.S. and other NATO forces, according to the statement issued after the defence committee meeting.

The Pakistani army said Saturday that NATO helicopters and fighter jets carried out an "unprovoked" attack on two of its border posts in the Mohmand tribal area before dawn, killing 24 soldiers and wounding 13 others. The troops responded in self-defence "with all available weapons," an army statement said.

Pakistan army chief Gen. Ashfaq Parvez Kayani condemned the attack, calling it a "blatant and unacceptable act," according to the statement.

'Hearfelt condolences'

"My most sincere and personal heartfelt condolences go out to the families and loved ones of any members of Pakistan security forces who may have been killed or injured," said Gen. John Allen, the top overall commander of U.S. and NATO forces in Afghanistan, in a statement.

The border issue is a major source of tension between Islamabad and Washington, which is committed to withdrawing its combat troops from Afghanistan by the end of 2014.

Much of the violence in Afghanistan is carried out by insurgents who are based just across the border in Pakistan. Coalition forces are not allowed to cross the frontier to attack the militants. However, the militants sometimes fire artillery and rockets across the line, reportedly from locations close to Pakistani army posts.

American officials have repeatedly accused Pakistani forces of supporting — or turning a blind eye — to militants using its territory for cross-border attacks. But militants based in Afghanistan have also been attacking Pakistan recently, prompting complaints from Islamabad.