"The number of killed is about 15 from both sides ... We have defeated the violent people who attacked the port town of Kismayo," Hassan Dhere, a commander of the Marehan unit, told AFP.
The fighting, between the Majerten and Marehan clans, broke out about 19km north of Kismayo, which is about 500km.
Residents said the clashes centered around the Golweyne area, with both sides exchanging heavy machinegun fire.
Hassan Mohamed Ali, a Marehan clan elder, said: "We have ejected criminals who were ambushing travelers from the Kismayo-Mogadishu road.
"We are still chasing them."
Meanwhile in Mogadishu, an army officer was killed and a second injured when their vehicle was hit by a roadside explosion, the latest in a string of attacks on government, African Union and Ethiopian troops.
Police fired shots in the air and made several arrests, witnesses said.
"The targeted government truck was completely destroyed," Colonel Ali Said, the police chief, said.
Violence has surged in Mogadishu since Somali government troops, backed by Ethiopian forces, ousted the Union of Islamic Courts group in April after months of fighting that left hundreds dead and hundreds of thousands displaced.
Somalia has been without a functioning central authority since the 1991 and the three-year-old transitional government has been unable to assert control.