The Pakistan army protested after two of its soldiers were injured in a clash with Nato helicopters in the Pakistani region of North Waziristan.
An army spokesman said Nato “violated Pakistan airspace” and demanded a meeting with Nato officials.
Western sources say the helicopters came under attack twice in Afghanistan before they opened fire. But local witnesses say the aircraft fired first.
It is not clear if the helicopters crossed the border.
The incident comes two weeks after al-Qaeda leader Osama Bin Laden was killed by US commandos in the Pakistani town of Abbottabad – prompting Pakistani condemnation.