Asked by the reporters on arrival at Kuwait Airport to confirm a newspaper report that Hamza Rabia was killed in a missile strike on Thursday, Musharraf said: "Yes indeed, 200 percent confirmed."
Musharraf said Hamza was killed "in North Waziristan", a tribal area on the Afghan border. "It is a place called Mirali, or little north of this town, that's the place," he said. "I think he was killed the day before yesterday (Thursday), if I am not wrong."
In Islamabad, Interior Minister Aftab Sherpao also confirmed the killing and made clear that Rabia was Egyptian.
"Al Qaeda operative Hamza Rabia, who was killed in the explosion, was an Egyptian national," Sherpao told AFP. "He was a very important al Qaeda commander."
"Five people were killed in the explosion and we have identified that one of them was Hamza Rabia. There were two other foreigners but we do not know their identities," he said.
Officials say the bodies of the two locals were found in the house, but that those of the foreigners, including Hamza, were believed to have been spirited away.
They said intelligence had intercepted inter-militant communications, according to which the man known as Nawab, a Hamza alias, had been killed.
But Al-Arabiya television said it had been contacted by a person claiming to be from al Qaeda denying that Hamza was dead.
"An official from the al Qaeda group has denied, in a telephone conversation with the Al-Arabiya channel, that Hamza Rabia has been killed," a presenter on the Arab satellite channel told viewers.
The caller said five people were killed in the explosion, but that they were two local men, two Tajiks and an Arab named Suleiman al-Moghrabi.
According to a CIA list of most wanted al Qaeda terrorists operating in Pakistan and Afghanistan seen by AFP, Hamza has a five million dollars bounty on his head.
Information Minister Sheikh Rashid said the explosion was not a result of any operation in the rugged region, where the army has been hunting for al Qaeda and Taleban fugitives.
The official Kuna news agency quoted Musharraf on Saturday as saying that his talks in Yemen will discuss efforts to improve intelligence co-operation in the fight against terrorism.
In Saudi Arabia, Musharraf will attend the summit meeting of the Organisation of the Islamic Conference (OIC).