Sheikh Rashid Ahmed, Pakistan's information minister, named the man as Abdul Rehman, one of the aliases used by Muhsin Musa Matwalli Atwah, for whom the US has offered a $5 million reward.
"He was involved in the Kenya bombing," Ahmed said on Thursday evening.
Pakistani military sources said Atwah was killed along with six other Muslim fighters in a missile attack by Pakistani Cobra helicopters on their hideout in North Waziristan tribal region just before midnight on Wednesday.
Egyptian-born Atwah, 41, has been indicted in absentia in the Southern District of New York for his alleged involvement in the bombings of the US embassies in Dar es Salaam, Tanzania, and Nairobi, Kenya, on August 7, 1998, the FBI's website says.
Atwah is believed to use several aliases, including Abd al-Rahman Al-Muhajir, Abdul Rahman, Abdul Rahman al-Muhajir, Abdel Rahman and Mohammed KA al-Namer.
A CIA list of most wanted al-Qaeda "terrorists" describes him as a senior explosives expert in the network.
Suspected al-Qaeda hideouts are
the target of Pakistani raids
"He is involved in multiple operations and may be knowledgeable of CBRN (chemical, biological, radiological, or nuclear)" attacks, the list seen by AFP said.
It described his location as being in Pakistan.
Wednesday's raid was the latest in a series of operations by the Pakistani army in the last few weeks against suspected fighters in lawless North Waziristan.
The fighters are thought to include members of Afghanistan's former ruling Taliban rulers as well as al-Qaeda fighters.