The al-Shabab militant group says it killed 27 soldiers in the raid, which began just after early morning prayers.
A Somali military officer said reinforcements had been sent to the area, about 50km (31 miles) from the port city of Kismayo, but did not give further details about the attack.
Al-Shabab has been waging an insurgency in Somalia for more than 10 years.
A 22,000-strong African Union force is in the country to help the government fight the al-Qaeda-linked militants.
The US military also has a presence of several hundred troops in Somalia to carry out special operations and to train government forces.
Some Somali government soldiers “fled into the jungles” following the attack on the base in Baar Sanguni, an al-Shabab spokesman, Abdiasis Abu Musab, said.
The sound of the blast and shooting was so loud that residents in the town of Jamame, about 70km from Kismayo, said they heard it, Reuters news agency reports.
“We heard a huge blast after early morning prayers. Then heavy exchange of gunfire followed. It was in the direction of Baar Sanguni,” resident Osman Abdullahi was quoted as saying.
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