Three Pakistani soldiers were killed in a Nato helicopter attack near the Afghan border, Pakistani officials say.
Security officials said Nato helicopters entered Pakistani airspace and targeted a paramilitary checkpoint.
Pakistani officials have now stopped Nato supply trucks from crossing the border at Torkham.
A Nato official confirmed there was an attack, but said that it believed it was in Afghan airspace. She added that the incident was under investigation.
Pakistani officials say they stopped the Nato trucks because of “security considerations”.
The BBC’s M Ilyas Khan in Islamabad says that this is is the second attack by Nato-led International Security Assistance Force (Isaf) helicopters on suspected fleeing militants in the country’s Kurram area since last weekend.
Map of northern Pakistan
On 28 September a similar strike took place in Kurram, witnesses say.
A day earlier, Isaf helicopters reportedly chased militants into the neighbouring region of North Waziristan, killing more than 30 of them.
Our correspondent says that the latest strikes have set a new pattern in the US-led “war on terror” in Pakistani tribal areas.
But it seems that coalition forces have now decided to start using the “hot-pursuit” option as well.
The strikes come after months of pressure from the western coalition urging Pakistan to launch a clean-up operation against militant groups in its North Waziristan tribal area.
Pakistan has argued that this would be difficult because troops are already spread too thinly to open a new front against the militants, especially when many soldiers have been helping out with recent flood relief operations.
Last week Pakistan protested after Nato forces crossed the border and killed about 50 alleged militants.
A Pakistani official told AFP news agency that Thursday’s attack was “unprovoked”.
“Nato helicopters entered our airspace and targeted a paramilitary checkpost killing three soldiers and wounding three others,” the official said.
Officials say the checkpost came under fire for about half an hour and three soldiers were wounded in addition to those killed.
Pakistani soldier handing out flood supplies Pakistan says that its forces have been over-stretched because of recent floods
Another official told the Reuters news agency that Pakistan would consider “response options” if Nato continued to violate its sovereignty.
In a statement, Nato said it had carried out an attack on suspected insurgents near a coalition base in the border area of Dand Patan district, in Afghanistan’s Paktiya province.
However, it said that the helicopter did not cross into Pakistani airspace, and that it was working with Pakistan “to ascertain if the two events are linked”.
Isaf spokeswoman Maj Sunset Belinsky said the helicopters did not cross into Pakistan from Paktia province, despite Pakistani military officials informing them that their border forces had been attacked.
“Isaf is working with Pakistan to ascertain if the two events are linked. The matter remains under investigation,” she said.