The presumed head of Al-Qaeda in east Africa, Fazul Abdullah Muhammad, was killed in Mogadishu, Kenya's police chief said on Saturday, confirming a report from Somali Islamist Shebab rebels, AFP reports.

Fazul Abdullah, 38, is thought to have planned the massive US embassy truck bombings in Nairobi and Dar es Salaam in 1998 and had a $5 million bounty on his head.

"We have received that communication from authorities in Somalia. We have been told that there were two terrorists who were killed in Somalia on Wednesday last week," Kenyan Police Commissioner Mathew Iteere told AFP.

Iteere said the identity of one of the two had "been given as Fazul Muhammad ... That is what we have been told by our counterparts in Somalia."

"One of the men that was killed near Mogadishu was Fazul Abdullah, may Allah bless his soul. He is not dead as thousands like him are still in the fight against the enemy of Allah," a senior Al Shebab commander had earlier this week told AFP on condition of anonymity.

Officials with the Somali Transitional Government (TFG) said the men were killed at a roadblock on Tuesday night.

"Our forces fired on two men who refused to stop at a roadblock. They tried to defend themselves when they were surrounded by our men," a TFG military commander, Abdikarim Yusuf, told AFP.

"We took their ID documents, one of which was a foreign passport," he said, adding that an investigation was underway.

The incident happened on the north western outskirts of the Somali capital, a regional security source said.