US action along the Pakistan border has raised tensions
The United States military says US and Afghan forces have exchanged gunfire with Pakistani troops across the border with Afghanistan.
A senior US military official says a five-minute skirmish broke out after Pakistani soldiers fired warning shots near two US helicopters.
No one was hurt in the incidents and the US maintains its troops did not cross the border from Afghanistan.
Cross-border action by US-led forces has angered Pakistan in recent weeks.
The latest incident took place along the Pakistani border with the eastern Afghan region of Khost, an area which is a hotbed of militant groups.
Forces from the US-led coalition and the Nato-led International Security Assistance Force (Isaf) patrol the frontier, but Pakistan has been angered by reported US operations across the border in pursuit of insurgents.
A BBC correspondent says the border between the two countries is very unclear and in effect is marked by a 3km-4km (2-2.5 mile) stretch of no-man's land.
Nato said the helicopters - which belong to its Isaf mission - came under fire from a Pakistani checkpoint.
A US Central Command spokesman, Rear Admiral Greg Smith, said Pakistani soldiers at the checkpoint were observed firing on two US OH-58 Kiowa helicopters that had been covering a patrol of Afghan and US troops about a mile (1.6km) inside Afghanistan.
"The ground forces then fired into the hillside nearby that checkpoint, gained their attention, which worked," he said.
"Unfortunately, though, the [Pakistani] unit decided to shoot down a hillside at our ground forces. Our ground forces returned fire."
However, the Pakistani military gave a different account.
In a statement, commanders said troops fired warning shots at the helicopters when they strayed over the Pakistan border.
"When the helicopters passed over our border post and were well within Pakistani territory, our own security forces fired anticipatory warning shots," a statement said.
"On this, the helicopters returned fire and flew back."
In New York, Pakistan's new president gave another version of events when he said that Pakistan forces had fired "flares" to warn the helicopters they were near the border.
Later, in an address to the UN General Assembly, President Asif Ali Zardari referred to the cross-border tension when he said that his country could not allow its territory to "be violated by our friends".
An Isaf spokesman said he believed the incident was a misunderstanding, but he was certain the helicopters had been operating on the Afghan side of the border.
The BBC's Syed Shoaib Hasan, in Islamabad, says that the border between Afghanistan and Pakistan is very unclear.
3 Sept: First reported ground assault by US troops in Pakistan - Islamabad responds furiously
15 Sept: Pakistani troops reportedly fire in air to stop US troops crossing in S Waziristan
17 Sept: Top US military chief Adm Mike Mullen visits Pakistan to calm tensions
16 Sept: Pakistan says it was not told of fresh US missile strike
22 Sept: Pakistani troops in fresh firing to deter US incursion into N Waziristan, officials say
25 Sept: Pakistani troops fire warning shots at Nato helicopters on border with Khost
There is an imaginary border called the Durand line which each side marks differently.
Pakistan says that the area of no-man's land along the border is its territory and Afghanistan makes similar claims.
Tension between Washington and Islamabad has risen since 3 September, when the US conducted a ground assault in Pakistani territory, its first, targeting what it said was a militant target in the tribal region of 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.