Al Shabab attacked the base in Janay Abdale, about 60 km to the west of the port city of Kismayu, early in the morning with a car bomb and gunfire, Major Abdullahi Hussein told Reuters from Kismayu.
He said the insurgents had cut communications in the area and that the army had sent reinforcements.
The Jubbaland government said regional and national forces had inflicted a "big blow" on al Shabaab but did not provide details. Casualty figures were not immediately available for either side.
Halima Osman said her husband, who survived the attack and managed to get out of the base, had called her with a colleague's phone.
"He told me they ran into the bush after the bombing and fierce fighting killed many of his friends and the military vehicles were burnt," she told Reuters.
Al Shabab confirmed it was behind the attack. "We control the base. We took all their weapons," it said in a statement.
Forces from Jubbaland had wrested control of Janay Abdale from al Shabab in January as part of the offensive which first began in the center of Somalia before spreading south.
Al Shabab, an affiliate of al Qaeda, has come under intense pressure from the military and allied clan-based militias, who launched a major offensive last year. But the group has repeatedly shown its ability to strike back with major attacks.
