The NATO helicopters violated Pakistani air space at the Admi Kot border post in North Waziristan Agency in the early hours this morning, chief Pakistani military spokesman Maj Gen Athar Abbas said.
"The troops at the post fired upon the helicopters and, as a result of exchange of fire, two of our soldiers received injuries," Abbas said.
The Pakistan Army lodged a "strong protest" over the incident and demanded a flag meeting, he said.
The incident occurred in Datta Khel region of North Waziristan, which has witnessed numerous missile strikes by US drones over the past few years.
The US describes the region as a safe haven for Taliban and al Qaeda elements who frequently target NATO forces across the border in Afghanistan. The injured soldiers were airlifted by a Pakistani helicopter to Miranshah, the main town in the region.
The International Security Assistance Force in Afghanistan said it was looking into reports of the air strike.
The border incursion came at a time when Pakistan-US ties have been hit hard by the American military raid in the garrison city of Abbottabad that killed Osama bin Laden on May 2.
The covert military operation embarrassed and humiliated the powerful Pakistan Army and intelligence service.
Islamabad described the raid as a violation of its sovereignty and reacted angrily to allegations by senior US officials about the complicity or incompetence of its security forces in failing to detect bin Laden's presence in Pakistan.
Pakistan retaliated against an incursion by NATO helicopters in September last year, which killed two Pakistani soldiers, by shutting down the main supply route for NATO forces in Afghanistan.
The route was reopened after the US tendered an official apology for the incursion.