The militants drove a truck loaded with explosives to the main entrance of the base in Bulogadud, about 70 kilometres (40 miles) from the port town of Kismayo and then attacked the soldiers.
"There was an attack on the military base in Bulogadud this morning... The initial information indicates that more than 10 soldiers were killed," Abdulahi Mohamed, a senior security official, said by phone.
"There was a car bomb blast and gunfire followed. The forces retreated from the base initially but they later regained control," he added.
"Some people in Bulogadud told us the militants looted the camp ... They burned down everything and left," Ahmed Mohamud, a resident said.
Shabaab claimed responsibility for the attack.
"The Mujahedeen fighters took control of Bulogadud, there were many enemy deaths and three technical vehicles were looted," a brief statement on a pro-Shabaab website said, citing the group's Andalus radio.
The Shabaab have sworn to overthrow Somalia's fragile government, which is kept in place with international support.
The Shabaab force was pushed out of the capital in August 2011 and lost most of its other bastions in Somalia.
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