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.
And it's clear that we (and NATO) are just NOT going to stop. Wonder if Obama will keep on keeping on? So am I. I wonder if Mr. Lehrer has that question prepared for tonight in case this debate goes off.
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.
With no clear statements of policy from either side, this is not in the control of anyone except local commanders.
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.