The attack is the latest in a string of assaults by the Al-Qaeda-affiliated insurgents, who last week stormed a base manned by the African Union forces in Somalia (AMISOM), killing dozens.
Heavy gunfire was reported late Sunday for several hours, with the Shebab briefly taking over the camp near Kismayo and beheading some of those captured before looting supplies and leaving, witnesses said.
"There was heavy fighting that left several of the soldiers dead," said security official Abdirashid Moalim, speaking from Kismayo.
The Shebab is fighting to overthrow Somalia's Western-backed government which is propped up and protected by the 22,000-strong AMISOM force.
On Friday, the Shebab attacked an AMISOM base in Lego village, 100 kilometres (62 miles) northwest of the capital Mogadishu, manned by around 100 Burundian soldiers.
The Shebab later boasted of having killed 80 soldiers, and carried off the bodies of 60 of them.
Witnesses reported seeing dozens of bodies, but there has been no formal confirmation of casualties and the toll was not possible to independently confirm.
The Islamic militants commonly step up their attacks during Islam's holy fasting month of Ramadan. On Wednesday six people were killed in a suicide attack in Mogadishu on a diplomatic convoy from the United Arab Emirates.
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