Reflecting the particularly gruesome nature of the attack, newly elected Prime Minister Raja Pervaiz Ashraf said he would complain directly to Afghan President Hamid Karzai.
"We have strongly protested and I will, too, God willing, talk about this to Karzai," said Ashraf, speaking in Karachi.
The Pakistani Taliban say their fighters carried out the raid, but the statement didn't say whether the attackers had crossed over from Afghanistan. It said Pakistani claims of militant casualties were false.
Both sides often release false or partial information about such events, which usually happen in areas inaccessible to the media.
The border region between Afghanistan and Pakistan is a hotbed of militant insurgency largely removed from the control of either government.
The deputy border police commander for eastern Afghanistan, Maj. Mohammad Ayub Hassainkhail, said the Pakistani military informed police Monday that one of their patrols was missing. He said they told the Pakistani officials they had no information about any Pakistani military near their checkpoints, but said it is a long border.
"They have plenty of militants on their side. Why would the militants cross over from Afghanistan? I strongly reject this claim that any militants crossed over from Afghanistan to Pakistan and did this," he said.
In a late Monday attack in southern Pakistan, Taliban gunmen fired on the offices of Aaj TV in the city of Karachi, injuring a guard and an employee, police official Abdus Salam Shaikh said.
Pakistani Taliban spokesman Ahsanullah Ahsan claimed responsibility for the firing and said it was carried out because Aaj did not broadcast the group's claim for the attack in Upper Dir. He warned that other media would be targeted if they failed to broadcast the Taliban's statements.
In another development in the troubled northwest, a top Pakistani Taliban commander in the South Waziristan tribal area said Monday that he would not allow any polio vaccinations in his territory until the U.S. stops drone attacks in the region. Maulvi Nazir said in an email to reporters that all organizations doing immunizations should stop immediately.
Earlier this month, another militant commander in North Waziristan also announced a ban of polio vaccinations. Pakistan is one of only three countries in the world where polio is still endemic. The virus usually infects children living in unsanitary conditions, attacks the nerves and can kill or paralyze.
Vaccination programs, especially those with international links, have come under suspicion in Pakistan ever since it became known that a Pakistani doctor ran a fake vaccination program to help the CIA track down Osama bin Laden. The al-Qaida leader was killed during a raid by U.S. Navy SEALs in the Pakistani city of Abbottabad in May 2011. Dr. Shakil Afridi had helped the CIA run a vaccination program designed to collect DNA from bin Laden and his family.
Associated Press writers Ishtiaq Mahsud in Dera Ismail Khan, Rasool Dawar in Peshawar and Rahim Faiez in Kabul, Afghanistan contributed to this report.