Repairing strained ties while keeping the pressure on al-Qaida and Taliban commanders leaders hiding in the lawless frontier area will be a key challenge for Barack Obama when he becomes U.S. president in January.
The latest attack took place in Kam Sam village in North Waziristan region, a stronghold for militants blamed for killing U.S. troops in Afghanistan and suicide blasts within Pakistan.
A Pakistani intelligence official said an agent who visited the village reported that 13 suspected militants were killed. The official said the targeted house belonged to a Taliban commander and that authorities were working to determine the identities of the dead.
A government representative in the region also put the death toll at 13.
The officials spoke on condition of anonymity because they were not authorized to talk to the media.
It was the first suspected American attack since Gen. David Petraeus took over as head of the U.S. Central Command on Oct. 31, giving him overall command of the wars in Iraq and Afghanistan. He visited Pakistan and Afghanistan this week.
In an interview with The Associated Press in Afghanistan on Thursday, Petraeus said the border strikes have killed three "extremist leaders." He did not identify the men.
There have been unconfirmed media reports that senior al-Qaida operatives Abu Jihad al Masri, described by the U.S. government as the terror network's propaganda chief, and Khalid Habib, a regional commander, died in missile strikes in Pakistan in October.
Similar attacks in the border region killed senior al-Qaida commander Abu Laith al-Libi in January and Egyptian explosives and poisons expert Abu Khabab al-Masri in July.
The rugged, mountainous region where the government has never had much control is considered a likely hiding place for Osama bin Laden and his No. 2 Ayman al-Zawahri.
There have been at least 18 missile strikes into Pakistan since August, more than three times as many as in 2007, apparently reflecting U.S. frustration at insufficient action by Islamabad against extremists.
Pakistan leaders said they asked Petraeus to call a halt to the strikes, which they said were angering residents, making it more difficult to get their cooperation with military offensives.
Petraeus said he would "take on board" what they said, but Pakistani officials said he gave them no promise the attacks would stop.
During the election campaign, Obama said he would attack al-Qaida targets in the border area if Pakistan was unwilling or unable to do so, suggesting he would not stop the strikes.
The frequency of the raids has led some analysts to speculate that Pakistani leaders have privately agreed to them on the understanding they will publicly criticize them - something denied by Pakistani officials.
Pakistan's elected leaders have little leverage with the United States to force it to stop the strikes because they need Washington's help to get the country out of a crushing economic crisis.
The Pakistani army is undertaking a major offensive in the border region against militants.
Late Thursday, Pakistani helicopters and jets killed 17 suspected militants in Taliban strongholds near the Afghan border, said Jamil Khan, the No. 2 government representative in the semiautonomous Bajur region.
Meanwhile, authorities exchanged three captured Taliban militants - including a deputy to Pakistani Taliban leader Baitullah Mehsud - for 10 military personnel held by insurgents.
Haji Afzal Khan, the mayor in northwestern Hangu district, said the prisoners were swapped Wednesday and that Mehsud's freed deputy Rafiuddin had assured authorities he would help with peace efforts.
Rafiuddin was captured in July and the soldiers were seized later that month. The government has made similar prisoner exchanges in the past.
