Somali police said on Saturday that Fazul Abdullah Mohammed, one of Africa's most wanted al Qaeda operatives, was killed in the capital of the Horn of Africa country earlier this week.
"We have confirmed he was killed by our police at a control checkpoint this week," Halima Aden, a senior national security officer, told Reuters in Mogadishu.
Mohammed was shot at the checkpoint in an exchange of fire with police, Aden said.
"He had a fake South African passport and of course other documents. After thorough investigation, we confirmed it was him, and then we buried his corpse," Aden said.
Mohammed was reputed to be the head of al Qaeda in east Africa, and operated in Somalia, which has been without an effective central government since the overthrow of dictator Mohamed Siad Barre in 1991.
The United States had offered a $5 million reward for information leading to the capture of the Comorian, who speaks five languages and is said to be a master of disguise, forgery and bomb making.
He is accused of playing a lead role in the 1998 embassy attacks in Nairobi and Dar es Salaam, which killed 240 people.
"He was killed on Tuesday midnight in the southern suburbs of Mogadishu at Ex-control police checkpoint. Another Somali armed man was driving him in a four-wheel drive when he accidentally drove up to the checkpoint," Aden said.
"We had his pictures and so we cross-checked with his face. He had thousands of dollars. He also had a laptop and a modified AK-47," he said.
Kenyan anti-terrorist police said they had been informed of Mohammed's killing by US sources.
"We received intelligence from within the US embassy that he (Mohammed) is dead. We ourselves do not yet have any evidence of his death," Kenya's Anti Terrorism Police Unit head Nicholas Kamwende told Reuters in Nairobi.