It is "highly likely" that Nato aircraft were behind a deadly overnight raid on a Pakistani border checkpoint, a Nato spokesman has told the BBC.
Brigadier-General Carsten Jacobson said Nato was investigating how the incident occurred and sent condolences.
Pakistan says at least 24 soldiers were killed. Prime Minister Yousuf Raza Gilani called it "outrageous".
Pakistan retaliated by blocking Nato supply convoys, and ordering a review of co-operation with the US and Nato.
It also demanded the US vacate the remote Shamsi airbase - though it has made a similar demand before and the base may already be empty of US personnel, a BBC correspondent says.
The night-time attack took place at the Salala checkpoint, about 1.5 miles (2.5 km) from the Afghan border, at around 02:00 local time (21:00 GMT).
Gen Jacobson said a combined force of Afghan and Nato troops were in the area when "a tactical situation developed on the ground", though he gave no more details.
He said close air support was called in, and "we're aware it's highly likely this caused casualties".
He said it was a high priority for Nato to "find out what happened".
Military sources told the BBC's Quentin Sommerville in Paktika province in Afghanistan that a US-Afghan special forces mission came under fire from a position within Pakistan.
They received permission from the headquarters of Nato's Isaf mission to fire back at what they believed was a suspected Taliban training camp.
The Pakistani army said in a statement that two border posts had been attacked by helicopters and fighter aircraft, killing 24 people and leaving 13 injured.
It said Pakistani troops fired back as best they could.
Chief of Army Staff General Ashfaq Parvez Kayani had strongly condemned the "blatant and unacceptable act", and demanded "strong and urgent action be taken against those responsible for this aggression", the military said.
A senior Pakistani military officer told Reuters the attack came "without any reasons" and that soldiers were asleep at the time.
Pakistani officials have told the BBC there was no militant activity in the area at the time.
In a statement, Isaf commander Gen John R Allen said the incident "has my highest personal attention and my commitment to thoroughly investigate it to determine the facts".
"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."
The incident looks set to deal a fresh blow to US-Pakistan relations, which had only just begun to recover following a unilateral US raid that killed Osama Bin Laden in Pakistan in May.
Prime Minister Gilani cut short a visit to his hometown to return to Islamabad, where he called an emergency meeting of the cabinet.
A foreign ministry statement said he was taking up the matter with Nato and the US "in the strongest terms".
Following the attack, lorries and fuel tankers were being stopped at Jamrud town in the Khyber tribal region near the city of Peshawar, officials and local media said - part of a key route supplying Nato equipment to Afghanistan.
"We have halted the supplies and some 40 tankers and trucks have been returned from the check post in Jamrud," Mutahir Zeb, a senior government official, told Reuters.
Pakistani troops are involved in fighting the Taliban in the crucial border region area. Hundreds of militants have been resisting attempts by the security forces to clear them from southern and south-eastern parts of the district.
In October, Pakistan's army chief Ashfaq Kayani warned the US against taking unilateral action in nearby North Waziristan.
Washington has for many years urged Islamabad to deal with militants in the area.