Pakistan's army lodged a "strong protest" over what it called an airspace violation after NATO helicopters exchanged fire with Pakistani troops at a military post early Tuesday.
The incident could further aggravate relations between the U.S. and Pakistan already strained over the American raid that killed Osama bin Laden more than two weeks ago.
Pakistani army officials said troops positioned at a guard post in the tribal area of North Waziristan fired on the NATO helicopters after the aircraft crossed the border from Afghanistan, and that two soldiers were injured by return fire.
The incident took place near an area thought to be a Taliban and al-Qaida sanctuary that has been targeted repeatedly by CIA drone strikes.
A Western military official in Kabul said two NATO helicopters supporting a base in eastern Afghanistan had returned fire and that details were being investigated.
"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 NATO coalition spokesman Lt. Col. John Dorrian.
He declined to say which coalition country was involved. But most of the helicopters that fly in that part of Afghanistan are American.
Pakistan has demanded a meeting with NATO officials to discuss the incident.
Last year, American helicopters killed two Pakistani soldiers near the border, mistaking them for insurgents. In response, the Pakistani government shut down NATO's main supply route for 11 days.
U.S.-Pakistan relations have since become so fraught that they have been pushed to the breaking point over the Navy SEAL strike that killed bin Laden in a Pakistani garrison town.
The Pakistani government is outraged that the U.S. carried out the operation without telling Pakistan first, and many American officials have expressed disbelief that bin Laden could have lived in the town of Abbottabad for at least five years without the authorities' knowledge. However, the U.S. has also said it has not found any evidence yet that Pakistani leaders knew of bin Laden's whereabouts.
The helicopter incident comes a day after U.S. Sen. John Kerry wrapped up a 24-hour visit to the capital, Islamabad, in which he worked to salvage the relationship with Pakistan. But the Massachusetts Democrat — the most high-profile American to visit Pakistan since the raid on bin Laden — also warned the government that "actions, not words" are needed to get ties back on track.
Kerry said Pakistan had agreed to immediately take several "specific steps" to improve ties, but he did not say what they were. The only tangible signs of progress were a remark by Kerry that Pakistan had agreed to give America the tail of a classified stealth helicopter destroyed by U.S. commandos when it malfunctioned during the raid, and a statement that Secretary of State Hillary Clinton would soon announce a trip to the country.
But there have also been signs of Pakistan's anger.
The Pakistani government sent the United States a written request following the bin Laden raid, asking Washington to reduce the number of American military personnel in the country, a U.S. military official, speaking on condition of anonymity because of the sensitivity of the issue, told The Associated Press.
There are currently more than 200 U.S. military personnel in Pakistan, some of whom are tasked with training Pakistani troops, the official said. Pakistan has asked the U.S. to reduce the number of trainers in the country, but the official would not specify the numbers involved.
With reporting from NPR's Julie McCarthy in Islamabad, Pakistan, and Quil Lawrence in Kabul, Afghanistan. Material from The Associated Press was used in this story.