Pakistan said its troops fired on two NATO helicopters that crossed the Afghan border Tuesday, and two of its soldiers were wounded in the skirmish.
The clash occurred early in the morning at Admi Kot Post in North Waziristan, a haven for Taliban attacks on coalition forces in Afghanistan.
NATO told The New York Times it was investigating the report, and could not immediately confirm whether the helicopters had entered Pakistani airspace.
The Pakistani Army said it "lodged a strong protest" and demanded a meeting with NATO.
A Pakistani security official in North Waziristan told The Washington Post 20 paramilitary troops were working at the post when shelling occurred. He said more troops were being sent to the area.
U.S.-Pakistan relations were already tense after the Navy SEAL raid that killed Osama bin Laden in Pakistan.
Tuesday's clash came as Pakistani Prime Minister Yousaf Raza Gilani flew to Beijing. Analysts saw the trip as a signal to Washington that Pakistan has alternative sources of military and economic aid.