The bloodshed on Sunday underscores the task facing a fledgling government trying to establish itself in the lawless Horn of Africa country after it was formed in the safety of neighbouring Kenya last year.
There was no clear word on what started the violence near the town of Hobyo 730km north of Mogadishu, but fighting between armed gangs in the area has killed up to 200 people and displaced thousands in recent months in disputes over land and blood feuds.
Residents said Sunday's clash, like recent ones, pitted fighters of the Saad wing of the Habr Gedir sub-clan of the Hawiye, Somalia's commercially most powerful clan, against the Habr Gedir's Sulaiman wing.
The fighting erupted at the villages of Hin-dawaco, Megajib and Saqiirro, 18km outside Hobyo and then spread into Hobyo itself, forcing more than 5000 terrified residents to flee, witnesses contacted by radio said.
Somalia, a country of about 10 million, has since 1991 been carved up into fiefdoms run by regional commanders.
Somalia's new President Abd Allah Yusuf and Prime Minister Muhammad Ali Gidi, both of whom are still based in Nairobi, toured areas in Somalia in late February and early March to prepare for the return of their government, which intends to disarm the country's many militias.