Rockets fired during battles between U.S.-led international forces and insurgents in Afghanistan killed 10 people in neighboring Pakistan Saturday.
"Pakistan has issued a strong protest over the incident," spokesperson Tasnim Aslam said, denying media reports that the operation had been agreed upon with Pakistani authorities.
"Pakistan does not want any NATO operations on its side of the border," she said. "Any operations on Pakistani territory are conducted by the Pakistani Army."
Some media reports said that NATO also conducted several air raids on Pakistan's tribal areas close to the Afghan border, killing 30 to over 40 people.
NATO officials have not commented on the strikes so far.
Pakistan became a key U.S. ally in fighting terrorism after it dropped its support for the Taliban and allowed U.S. troops to use its air bases and share intelligence during the war that toppled the Islamist movement in Afghanistan in 2001.
But the country has been pressured to step up its fight against Taliban- and Al Qaeda-connected militants who easily cross the ill-defined border to find shelter in Pakistan's tribal areas, which they use to stage attacks against Afghan and international forces in Afghanistan.