Pakistan's army has lodged a strong protest and demanded talks with NATO commanders after an allliance helicopter hit a Pakistani checkpoint, injuring two security personnel.
"It [the incursion] happened early morning," a Pakistani intelligence official, who declined to be identified because he was not authorised to speak to the media, told the Reuters news agency.
"The helicopter hit a Pakistani checkpoint on the border in the Datta Khel area."
A Western military official in Kabul, told Reuters that two NATO helicopters supporting a base in eastern Afghanistan had returned fire after being attacked from Pakistan.
Pakistan's military said it had sought a meeting with NATO commanders over the incursion, which came a day after US senator John Kerry met Yusuf Raza Gilani, Pakistan's prime minister, amid tensions in the country's relations since the killing of Osama bin Laden earlier this month.
Pakistan has condemned the US for conducting that operation in violation of its national sovereignty.
Tuesday's incident came hours before Yusuf Raza Gilani, the Pakistani prime minister, arrives in China on a visit seen by some as a diplomatic effort to seek closer and more productive ties with another major power.
Many fighters loyal to al-Qaeda, including foreign ones, are based in Datta Khel, a frequent target of US drone strikes. The place is also a stronghold of fighters loyal to Hafiz Gul Bahadur, a key Pakistani Taliban commander.
A drone attack in the same place on Monday left seven suspected fighters dead, Pakistani officials said.
A Western military official said Tuesday's operation started before dawn, when a NATO base in Afghanistan came under intermittent direct and indirect fire from the Pakistani side of the border.
Two helicopters flew into the area to provide support, one of which fired across the border after being fired at twice from the Pakistani side, the official said.
In a statement, the Pakistani army said its troops fired on a helicopter after it entered Pakistani airspace in the early hours of the morning. Two of its troops were injured when the helicopter returned fire, it said.
NATO, which confirmed the incident, said it was still trying to determine whether the helicopter crossed into Pakistani airspace, Lieutenant Colonel John Dorrian, the NATO spokesman, said.
"We're investigating the incident to determine a flight path by examining GPS waypoints in the helicopter computer, to construct a sequence of events and ultimately determine what led to the exchange of fire," said Dorrian.
He declined to say which coalition country was involved. But most of the helicopters that fly in that part of Afghanistan are American.
Dorrian said NATO would work with the Pakistani government to determine what happened, saying they expect it will reflect the same good co-operation seen in recent military operations along the border.
In recent weeks, NATO and Pakistan have launched co-ordinated offensives against fighters loyal to al-Qaeda on their respective sides of the border.
"This is going to be transparently looked into," Dorrian said.
North Waziristan is the base of the Haqqani network, a group of fighters allied to the Taliban which NATO says is fuelling the conflict in neighbouring Afghanistan. US-led drone aircraft have repeatedly targeted the area over the past year.