Pakistan says its troops fired warning shots at two Nato helicopters as they crossed the border from Afghanistan.
It is the first time the Pakistan army has admitted opening fire near US or Nato forces, as tension grows over cross border military action.
Nato said its aircraft were not in Pakistani airspace when shots were fired over Khost province.
The Pentagon said they were US helicopters and that Pakistan would have to explain what had happened.
Chief Pakistani military spokesman Major General Athar Abbas said that the helicopters had "crossed into our territory in Ghulam Khan area".
"They passed over our checkpost so our troops fired warning shots," he said.
He added that the matter was being taken up with the Nato-led International Security Assistance Force (Isaf) in Kabul.
However, Pakistan's new president, Asif Ali Zardari, appeared to contradict his military spokesman, insisting that his troops had only fired "flares" to warn the helicopters they were near the Pakistan border.
The BBC's Syed Shoaib Hasan, in Islamabad, says that the border between Afghanistan and Pakistan is very unclear.
There is an imaginary border called the Durand line which each side marks differently.
Our correspondent says that, in reality, the border is marked by a 3-4km (1-2 mile) stretch of no man's land.
Pakistan says that this is its territory and Afghanistan makes similar claims.
In a statement, Isaf said its helicopters had received small-arms fire from a Pakistan military checkpoint along the border near Tanai district, Khost, on 25 September "while conducting routine operations in Afghanistan".
"At no time did Isaf helicopters cross into Pakistani airspace," it added.
Pentagon spokesman Bryan Whitman said: "The flight path of the helicopters at no point took them over Pakistan."
He said US and Nato officials were speaking to their Pakistani counterparts to determine what had happened and to ensure there was no recurrence.
"The Pakistanis have to provide us with a better understanding of why this took place," he said.
Local tribesmen in the area told the BBC that two helicopters were trying to cross into Pakistani territory near Ghulam Khan, in North Waziristan, when Pakistani troops at posts near the border fired at them.
There are currently two Western military operations in Afghanistan - a US-led coalition and the Nato-led Isaf mission.
It appears the helicopters involved in Thursday's incident were US OH-58 reconnaissance aircraft operating under the Nato flag.
The BBC's Martin Patience, in Kabul, says it is believed to be the first time Nato helicopters have been fired on in this fashion.
The Afghan-Pakistan militant nexus
US attacks raise stakes in Pakistan
Correspondents say there is growing anger in Pakistan at US forces in Afghanistan allegedly violating Pakistani sovereignty.
The remote Afghan-Pakistani frontier is rife with militant groups.
BBC defence correspondent Rob Watson says the US doubts Pakistan's capability - and even willingness in some quarters - to tackle Islamic extremists.
There has been growing tension between the two countries since 3 September when the US conducted its first ground assault in Pakistani territory on what it said was a militant target in South Waziristan.
Pakistan reacted angrily to the action, saying 20 innocent villagers had been killed by US troops.
Local officials have said that on two occasions since then Pakistani troops or tribesmen have opened fire to stop US forces crossing the border. The claims were not officially confirmed.
On Wednesday, a drone believed to be operated by the CIA crashed inside Pakistan.
The US and Nato have called on Pakistan to do more to curb militants operating in the border area.
Oh great. This is just what we need.
But really, it's not the first time US troops (Not NATO, because It's just the US flying around) causing shit like we pantsless own the world. It's about time someone said "pants you".