The suspect, thought to be Saudi-born Abu Marwan al-Suri, was killed on Thursday close to the Afghan border.
Major-General Shaukat Sultan, the Pakistan army spokesman, said al-Suri was in a vehicle on the outskirts of Khar, a town near the Bajur tribal region.
Al-Suri opened fire when he was asked to stop his vehicle at a roadblock. He killed a Pakistani security official and wounded two others before he himself was killed.
His body has been transported to a hospital in the city of Peshawar for identification.
Intelligence sources said initial information indicates that the suspect was a close associate of Ayman al-Zawahiri, the number two leader of al-Qaeda.
Authorities found a video camera, a laptop computer, hand grenades and some documents in the suspect's vehicle, the officials said.
A Pakistani intelligence official said al-Suri was not thought to be the man's real name.
Damadola was struck by a US
missile aimed at al-Zawahiri
He said the suspect was believed to be among several al-Qaeda suspects previously thought killed in January in a US missile strike in Damadola village in Bajur, that had been aimed at al-Zawahiri.
Pakistani intelligence said that al-Zawahiri was not at the scene of the attack.
Osama bin Laden and his top deputy al-Zawahiri are thought to be hiding in Pakistan's tribal areas, near the border with Afghanistan.
Meanwhile on Thursday, seven Pakistani troops were killed and 22 wounded in an ambush in the North Waziristan tribal region.
Sultan said at least five militants were killed in subsequent fighting with security forces.
Thursday's ambush took place near where the Pakistani military killed seven terror suspects on April 12, including Mohsin Musa Matawalli Atwah, 45, an Egyptian on the FBI's list of most-wanted terrorists.
Atwah was wanted for alleged involvement in 1998 bombings of US embassies in Tanzania and Kenya that killed more than 200 people, including 12 Americans.