Pakistan's foreign ministry has said it has lodged a "strong protest" with Nato and the Afghan military after a border skirmish left a Pakistani soldier dead.
At least eight Taleban militants were also killed during the clashes which began when an Afghan border post was attacked before dawn on Wednesday.
During the battle, Nato forces fired shells and carried out an incursion into the Bajaur tribal region, it said.
Nato has not been granted permission to pursue militants over the frontier.
The Pakistani government warned earlier this year that unauthorised incursions by foreign troops would be treated as an invasion.
At a news conference, Pakistani foreign ministry spokesman Mohammad Sadiq said Nato and Afghanistan had insisted their troops had only deliberately targeted the militants who initiated the attack.
"We have lodged a strong protest with the Afghan and Isaf (Nato-led International Security Assistance Force) side and told them in clear terms that such incidents must not be repeated," he said.
"We emphasised that military action on Pakistan side is the exclusive responsibility of Pakistani forces," he added.
The US military has in the past, however, launched several missiles targeting Islamist militants based in Pakistan.
A senior al-Qaeda leader in Afghanistan, Abu Laith al-Libi, is believed to have been killed in a such a strike in North Waziristan in January.