Mohammed was reputed to be the head of al Qaeda in east Africa, operated in Somalia and is accused of playing a lead role in the 1998 embassy attacks in Nairobi and Dar es Salaam, which killed 240 people.
Police said they shot Mohammed at a checkpoint in Mogadishu after an exchange of fire at midnight on Tuesday.
Washington says several al Qaeda members involved in the embassy bombings sought sanctuary in neighbouring Somalia, where Islamist al Shabaab insurgents, who claim links to al Qaeda, are fighting a weak Western-backed administration.
Somalia has been without an effective central government since the overthrow of dictator Mohamed Siad Barre in 1991.
"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.
"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.
The United States had offered a $5 million reward for information leading to the capture of the Comorian, who spoke five languages and was said to be a master of disguise, forgery and bomb making.
U.S. Secretary of State Hillary Clinton hailed the killing.
"Harun Fazul`s death is a significant blow to al Qaeda, its extremist allies, and its operations in East Africa," she told reporters while on a visit to Dar es Salaam, Tanzania.
"It is a just end for a terrorist who brought so much death and pain to so many innocents in Nairobi and Dar es Salaam and elsewhere -- Tanzanians, Kenyans, Somalis and our own embassy personnel."
A senior U.S. official in Washington added that his killing removed one of the group "most experienced operational planners in East Africa and has almost certainly set back operations".
U.S. officials say Mohammed, believed to be in his mid 30s, also masterminded an attack on an Israeli-owned hotel along Kenya`s coast in November 2002 that killed 15 people. (*)
Editor: Kunto Wibisono
Copyright © ANTARA 2011
