The fighting erupted Friday afternoon and continued into the evening and the morning hours of Saturday, locals said.
Intense street battles in Mogadishu's Bondhere and Hodan districts claimed at least 12 lives and wounded 13 persons, most of whom were civilians.
Medical workers at Mogadishu's Daynile, Keysaney and Medina hospitals reported treating critically wounded civilians.
It was not clear how many casualties were sustained by the fighting sides. The battles were between African Union peacekeepers (AMISOM) and Al Shabaab insurgents who control many regions in south-central Somalia.
Nomads fight Shabaab
Armed nomads fought against Al Shabaab insurgents in Middle Shabelle region, local reports say.
At least 10 people including six Al Shabaab fighters were killed during Friday’s battles in Warsheikh, a town in Middle Shabelle region north of Mogadishu.
Witnesses said the fighting erupted after nomad clan fighters rejected Al Shabaab's order to hand over a suspected killer. At least 12 people were wounded during the fighting.
It is not the first time that locals have taken up arms against Al Shabaab insurgents in southern Somalia. In Mogadishu recently, locals fought against Al Shabaab after the insurgents refused to give residents food aid.
Mogadishu has been torn by an insurgency since early 2007 with Al Qaeda-affiliated Al Shabaab aiming to topple Somalia's Western-backed TFG interim government.