Aden Abdulkadir, commander of the first division of Jubbaland forces, said the operation was conducted in Yaq Baisharo, on the outskirts of the coastal city of Kismayo.
"There was a fierce clash and the forces inflicted severe casualties on the militan’ts, killing three of them. We captured one of the fighters alive," he said.
The troops also recovered weapons from the militants, Abdulkadir said.
Eyewitnesses told Xinhua that they heard fierce gunfire that lasted hours.
"Militants were attacked by heavily armed government forces," said Siham Hashi, a local resident.
On Tuesday, Somali special forces killed 35 al-Shabab fighters in another operation in the same region.
Somali troops have intensified operations against al-Shabab in southern regions where the militants still hold swathes of rural areas, carrying out ambushes and planting landmines.