The Pakistani government has given the US fifteen days to vacate an airfield in Balochistan province after an alleged cross-border attack which killed 25 Pakistani soldiers.
The attack on a military checkpoint in northwest Pakistan also wounded at least a dozen soldiers.
A spokesman for the NATO-led alliance in Afghanistan confirmed on Saturday that it was "highly likely" the alliance's aircraft killed Pakistani soldiers.
"Such cross-border attacks cannot be tolerated any more. The government will take up this matter at the highest level and it will be investigated"
- Masoud Kasur, governor of Khyber
"Close air support was called in, in the development of the tactical situation, and it is what highly likely caused the Pakistan casualties," General Carsten Jacobson, a spokesman for the NATO-led International Security Assistance Force (ISAF), told the Reuters news agency.
The incident prompted Pakistan to summon the US ambassador in Islamabad, lodge a protest with NATO, and shut a vital supply route for NATO troops fighting in Afghanistan.
The Pakistani government also gave the US fifteen days to vacate Shamsi air base. Pakistan made a similar demand earlier this year, following the raid which killed Osama bin Laden.
The decision came after Yousuf Raza Gilani, the Pakistani prime minister, called an emergency meeting of his military chiefs. The foreign ministry also summoned Cameron Munter, the US ambassador in Islamabad, to "lodge a strong protest" against the attack.
"The foreign secretary conveyed to the US ambassador that the unprovoked attack by NATO/ISAF aircrafts on border posts in which 25 Pakistani troops lost their lives and another 13 were injured had deeply incensed the government and the people of Pakistan," the ministry said in a statement.
The Obama administration pledged to conduct a full investigation into the attack.
Secretary of State Hillary Clinton and Defence Secretary Leon Panetta in a joint statement on Saturday said they had each spoken to their Pakistani counterparts to express their condolences for the loss of life and expressed their full support for "NATO's intention to investigate immediately."
A Pakistani government official said the dead from Friday night's attack in the Mohmand tribal area included two officers.
The checkpoint that was attacked had been recently set up in the Mohmand tribal area by the Pakistan army to stop Taliban fighters holed up in Afghanistan from crossing the border and staging attacks, said two government administrators in Mohmand, Maqsood Hasan and Hamid Khan.
NATO supply trucks and fuel tankers bound for Afghanistan were stopped at Jamrud town in the Khyber tribal region near the city of Peshawar hours after the raid, officials said.
"We have stopped NATO supplies after receiving orders from the federal government," said Mutahir Hussain, a senior administration official in Khyber. "Supply trucks are being sent back to Peshawar."
Pakistan is a vital land route for 49 per cent of NATO's supplies to its troops in Afghanistan, a NATO spokesman said.
The incident occurred a day after US General John Allen met Pakistani Army Chief of Army Staff General Ashfaq Pervez Kayani to discuss border control and enhanced co-operation.
Friday's attack is expected to further worsen US-Pakistan relations, already at one of their lowest points in history, following a tumultuous year that saw the bin Laden raid, the jailing of a CIA contractor and US accusations that Pakistan backed an attack on the US Embassy in Kabul.
An increase in US drone strikes on armed groups in the last few years has also irritated Islamabad, which says the campaign kills more Pakistani civilians in the border area than fighters.
Washington disputes that, but declines to discuss the drone campaign in detail.
"This is an attack on Pakistan's territorial sovereignty," said Masoud Kasur, the governor of Pakistan's northwestern Khyber-Pakhtunkhwa province.
"Such cross-border attacks cannot be tolerated any more. The government will take up this matter at the highest level and it will be investigated."
In a telephone conversation with US Secretary of State Hillary Clinton, Pakistan's Foreign Minister, Hina Rabbani Khar said attacks like Saturday's were "totally unacceptable. They demonstrate complete disregard for international law and human life, and are in stark violation of Pakistani sovereignty".
Khar's office said Sunday's early morning telephone conversation conveyed Pakistan's "deep sense of rage" over the air strikes. Khar said the attack "negates the progress made by the two countries on improving relations and forces Pakistan to revisit the terms of engagement."