Pakistan lodged a protest with NATO and Afghan forces on Monday, accusing them of failing to act against militant safe havens in Afghanistan after a cross-border attack killed 13 Pakistani troops, a military official said.
The move is likely to intensify tensions between troubled allies Islamabad and Washington, currently involved in difficult talks to repair ties.
More than 100 militants based in Afghanistan's Kunar province entered Pakistan and attacked a military patrol on Sunday, the military official said. Fourteen militants and six soldiers were killed in the skirmish.
Seven Pakistani soldiers were beheaded by militants after the clash and four were still missing, the official said.
Foreign Ministry said the Afghan deputy head of mission in Islamabad was summoned and presented with a "strong protest".
The Malakand faction of the Taliban claimed responsibility, and threatened more attacks.
"Our fight will continue until the establishment of sharia law in Pakistan ... We will fight whoever tries to stand in our way," Sirajuddin Ahmad, the faction's spokesman, told Reuters.
Ahmad claimed the group had killed 17 Pakistani soldiers.
The NATO-led International Security Assistance Force in Afghanistan said it was aware of the report, but had no information.
Fazlullah Wahidi, governor of Kumar province, said militants were based in Pakistan, not Afghanistan. "We don't have any information about militants crossing the border from Afghanistan to attack troops in Pakistan," he told Reuters.
The Malakand, or Swat, Taliban are led by Maulvi Fazlullah, who was the Taliban leader in the Swat Valley, about 100 miles northwest of Islamabad, before a 2009 army offensive forced him to flee.
Also known as FM Mullah for his fiery radio broadcasts, he regrouped in Afghanistan and established strongholds, according to the Pakistan military.
Fazlullah re-emerged as a threat last year, when his fighters conducted cross-border raids that killed around 100 Pakistani security forces, angering Pakistan, which faces threats from multiple militant groups.
Pakistan wants Afghan and NATO forces to act against Afghanistan-based militant groups that cross the border to attack Pakistani forces and civilians.
The United States has repeatedly called on Pakistan to do away with what it calls safe havens for militants fighting NATO forces backing Afghanistan's government against the Taliban.
Defense Secretary Leon Panetta this month said Washington was reaching the end of its patience over the matter, but tempered those remarks in an interview with Reuters last week, saying both sides had to work at improving relations.
Islamabad rejects any U.S. suggestion that it is allowing insurgents to operate in Pakistan, saying it will not allow its territory to be used against any country.