The militant commander, Nazir, who was killed last Wednesday was also part of the Taliban but he led a faction that agreed to a cease-fire with the Pakistan military in 2009 and did not attack domestic targets.
As a result, while his death is likely to be seen in Washington as affirmation of the necessity of its controversial drone program, it could cause more friction in already tense relations with Pakistan.
Analysts say Nazir's killing is likely to complicate the Pakistani army's fight against the local and foreign al-Qaida linked militants holed up in the country's tribal region. They say his fighters may turn their guns toward Pakistani troops and may join the Pakistani Taliban's fight against the state.
Still, Nazir outraged many Pakistanis in June when he announced that he would not allow any polio vaccinations in territory under his control until the U.S. stops drone attacks in the region.
Washington wants Pakistan to launch a military operation in North Waziristan, believed to be the last stronghold of many of the militant groups. But Islamabad had been refusing, saying it does not have enough troops and resources to do that.
In absence of such an operation, the U.S. relies more on drone strikes to take out militants. The program has killed a number of top militant commanders including Abu Yahya al-Libi, who was al-Qaida's No. 2 when he was killed in a June strike.
Associated Press Writer Rasool Dawar in Peshawar, Pakistan contributed to this report.