In an apparently unrelated attack, a bomb blew out a wall of a government official's office in Peshawar, the last big city on the route to Afghanistan, early on Thursday, police said. There were no reports of casualties.
Also in the eastern Afghan province of Logar, unknown gunmen abducted seven Pakistani engineers in Pul-e Alam, said provincial police chief Gulam Sakhi Rogh Lewanai.
The United States has long wanted Pakistan, whose military and economy depend heavily on billions of dollars in American aid, to crack down on militant groups that cross its unruly border to attack Western forces in Afghanistan.
More recently, U.S. Secretary of State Hillary Clinton asked Pakistan to bring all militant groups to the negotiating table in order to stabilize Afghanistan.
The NATO attack makes Pakistani cooperation less likely.
NATO hopes an investigation it promised will defuse the crisis and that confidence-building measures can repair ties.
Critics say Pakistan has created a deadly regional mess by supporting militants like the al Qaeda-linked Haqqani network to act as proxies in Afghanistan and other groups to fight Indian forces in the disputed Kashmir region.
Pakistan says it has paid the highest price in the war on militancy. Thousands of soldiers and police have been killed.
"The sacrifices rendered by Pakistan in the war on terror are more than any other country," Khar was quoted as saying. "But that does not mean we will compromise on our sovereignty."