Musharraf, arriving in Kuwait at the start of a three-nation visit to the Middle East, said on Saturday that Hamza Rabia was among five people killed in an explosion on Thursday in North Waziristan, a tribal region bordering Afghanistan.
"Yes, indeed, 200% confirmed," Musharraf said.
But Dubai-based satellite TV channel Al-Arabiya said on Saturday that it had been contacted by a person claiming to be from al-Qaida who denied that Rabia had been killed.
"An official from the al-Qaida group has denied, in a telephone conversation with the Al-Arabiya channel, that Hamza Rabia has been killed," a presenter on the channel told viewers.
The Al-Arabiya presenter cited the caller as saying that five people were killed in an explosion in the tribal region, but these were two local men, two Tadjiks and an Arab called Sulayman al-Maghrabi.
A Pakistani intelligence official, speaking on condition of anonymity, said Rabia was believed to have been the operational commander of al-Qaida fighters in North Waziristan and adjoining South Waziristan.
The explosion near North Waziristan's main town, Miran Shah, was triggered as suspected Islamist fighters were making a bomb, Syed Zaheerul Islam, a government administrator, said on Thursday.
Islam said the blast also killed four other people, including two area residents, and injured two others, who have not been identified.
One report says Rabia was killed
in a village east of Miran Shah
In another report, Pakistan's Dawn newspaper said on Saturday that Rabia, believed to be of Syrian origin, was killed in a missile attack on a mud-walled home in Isori, a village east of Miran Shah.
The attack may have been launched from two unmanned aircraft, or drones, the newspaper said, citing unidentified sources.
Associates, who were also from outside Pakistan, retrieved the bodies of Rabia and two other foreigners and buried them in an unknown location, the report said.
Military officials have said hundreds of Arab, Afghan and Central Asian fighters are in North and South Waziristan. Pakistan - a key ally of the United States in its war against terrorism - has deployed thousands of troops in the area.