According to eyewitness and militia accounts, the militants and civilians were killed on Friday and Saturday in the fierce fighting between the Ras Kamboni militia and its rivals led by Barre Hirale, who is reportedly backed by the government in Mogadishu.
Hirale said that at least 50 fighters from both sides and civilians had been killed in the fighting.
Bile Mohamed, a shopkeeper in central Kismayo, said he had counted nine dead bodies on a Kismayo road.
Hussein Ali, a resident from another area of Kismayo, said he saw 12 dead bodies.
“I am afraid scores died in the alleys and inside houses,” said Ali.
However, both men said that fighting had stopped now.
“At the same time as this new fighting has broken out, contacts are underway to put together an inclusive process to defuse tensions,” said Nicholas Kay, the top UN diplomat in Somalia.
He added that fighting would entrench positions and “make it all the harder to achieve a settlement”.
African Union troops are currently in charge of security in the lucrative port of Kismayo and its fertile hinterlands.
In October 2012, Kenyan troops backed by Ras Kamboni militiamen, captured the city from al-Shabab fighters.
On June 8, a senior al-Shabab official in Kismayo said Kenya was responsible for the bloodshed.
“The resurgence of tribal hostility in Kismayo is a result of the Kenyan invasion of the city and the Kenyan government will be held fully responsible for every drop of blood,” Sheikh Xudayfa Abdirahman stated.
Somalia has not had an effective central government since 1991, when warlords overthrew former dictator Mohamed Siad Barre.
However, MPs meeting in Mogadishu elected Hassan Sheikh Mohamud as the new president of Somalia with a big majority in September 2012.
The weak Western-backed government in Mogadishu has been battling al-Shabab fighters for more than five years and is propped up by a 10,000-strong African Union force from Uganda, Burundi, Djibouti, and Kenya.