Details of the clashes that sparked the apparent air strike remain unclear
Pakistan's military has condemned an air strike by Afghanistan-based US forces that killed 11 of its troops as a "cowardly attack".
The incident happened inside Pakistan, near the border with Afghanistan, as US-led forces tackled pro-Taleban militants.
The US military confirmed it had used artillery and air strikes after coming under fire from "anti-Afghan" forces.
It comes amid rising tensions between the US and Pakistan militaries.
The soldiers' deaths occurred overnight at a border post in the mountainous Gora Prai region in Mohmand, one of Pakistan's tribal areas, across the border from Afghanistan's Kunar province.
Eight Taleban militants were also killed in the clashes, a Taleban spokesman said.
'Act of aggression'
In a statement, the Pakistani military quoted a spokesman who condemned "this completely unprovoked and cowardly act".
The spokesman said the incident "hit at the very basis of co-operation and sacrifice with which Pakistani soldiers are supporting the coalition in the war against terror" and added that the army had launched a "strong protest".
The BBC's Barbara Plett in Islamabad says the statement was very strongly worded, describing the incident as an "act of aggression".
A similar government statement condemned the "senseless use of air power" as "totally unacceptable".
The US military said in a statement that coalition forces had been engaged by "anti-Afghan forces" near the checkpoint and fired artillery rounds at the militants.
It said the operation it was carrying out at the time had been co-ordinated with Pakistani forces, and that it was investigating the incident.
Maulvi Umar, spokesman for a pro-Taleban militant group in Pakistan, told the BBC: "The Afghan army and the US troops there were trying to set up a checkpost on the border.
"So we launched an attack on them from several sides and caused serious harm - and then the US and Nato forces began a series of air strikes."
A spokesman for the Nato-led International Security Assistance Force (Isaf) in Afghanistan told the BBC that its troops had been fired on from across the border and retaliated by firing back.
Both US forces and Nato-led coalition forces are operating in Afghanistan, with Nato focused mainly on peacekeeping and reconstruction and the US troops working more directly to combat militant activity.
Alleged US missile strikes have sparked anger in Pakistan
The US has in the past launched missile strikes into Pakistani territory from unmanned aircraft, although it does not officially confirm such attacks.
Our correspondents says these strikes have caused anger in Pakistan as they are widely seen as a violation of its sovereignty, and there has been a lot of disquiet in Pakistan during the past month over the issue.
She says that if one of these air strikes is confirmed to have killed some Pakistani soldiers, it will certainly not help US-Pakistan relations, which some analysts say seem to be at their lowest ebb since the 11 September 2001 attacks on the US.
Pakistani troops have been killed in "friendly fire" on the border with Afghanistan on several occasions in the past.
But the latest is thought to have been the most deadly single incident.
Taleban fighters have a strong presence in the border areas of the tribal districts and local administrators have little power there, although security forces keep a presence on the border posts.
Afghan and US-led forces accuse Islamabad of failing to stop infiltration by Taleban fighters who take refuge in Pakistan's tribal belt along the frontier, and are worried that the Pakistani government's recent peace talks with militants there will only give the Taleban more room for manoeuvre.
Late on Tuesday, Pakistan's military denounced a report by the US-funded Rand corporation accusing Pakistan's intelligence services and its paramilitaries of supporting Taleban insurgents with information and training.
The Pakistani military dismissed the claims as "factually incorrect" and "yet another smear campaign maligning Pakistan armed forces".
Meanwhile, in a separate incident, three women and a child were killed in an operation by US-led forces in south-eastern Afghanistan targeting militant leaders, the coalition said.
An Interior Ministry spokesman told the Associated Press 31 people had died, mostly militants. The death tolls could not be verified.