"The army is in full control" of the port of Barawe, 200 kilometres southwest of Mogadishu, the Somali military official Abdi Mire said.
"The situation is calm, the militiamen had fled before the forces reached the town," said the provincial governor Abdukadir Mohamed Nur. "They could not put up resistance and have emptied their positions."
The Shebab, Al-Qaeda's main affiliate in Africa, exported charcoal through Barawe to Gulf countries, earning at least USD 25 million a year from trade according to UN estimates.
The Shebab have vowed to avenge his death and continue their fight to topple the country's internationally backed government.
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Yesterday, a Shebab commander, Mohamed Abu Abdallah, vowed that the militia would maintain pressure on Somali and AU forces even if they took Barawe.
"Let me assure you that we will never leave around Barawe, the fighting will continue and we will turn the town into graveyards of the enemy," he said, quoted by a pro-Shebab website.
The 22,000-strong AMISOM force, with soldiers drawn from six nations, have been fighting alongside government troops against the Shebab since 2007.