* Tensions already high over rivals for regional presidency
* Flare-up in Kismayu raises worries of broader fighting
* Somalia slowly emerging from two decades of conflict
By Abdi Sheikh
MOGADISHU, June 26 (Reuters) - At least three people were killed in a brief skirmish between rival militias in southern Somalia, witnesses said, the second deadly flare-up so far this month in the disputed strategic port of Kismayu.
The clash between the Ras Kamboni militia and Marehan clan fighters has heightened tensions in a city already divided by rivals claiming the presidency of Kismayu and the southern Jubaland region and raises worries of a broader conflict.
Somalia has been slowly emerging from two decades of war that have left the Horn of Africa nation in ruins, but Western governments and analysts say renewed fighting between warlords or resurgent Islamists could swiftly reverse the fragile gains.
Witnesses speaking to Reuters by telephone from the port said Ras Kamboni fighters opened fire on a car used by members of the Marehan clan in central Kismayu, where boundaries between rival factions have been drawn after the last bout of fighting.
"Ras Kamboni militia near the hospital opened fire on another militia car passing by at a junction," said one resident Jamac Hilowle. "I could see three dead people."
The Ras Kamboni seized the car, the bodies of those killed and their weapons, prompting a short-lived counter-attack by the Marehan that was pushed back, said witnesses. Roads were deserted and businesses shut up shop.
Earlier clashes on June 8 killed 18 people, said witnesses. Human Rights Watch, citing U.N. figures, put the death toll at 31.
Kismayu was controlled by Islamist al Shabaab rebels until last September when the militants fled an offensive by Kenyan troops supported by Ras Kamboni, a militia group loyal to a former governor of Kismayu, Ahmed Madobe.
A local assembly last month declared Madobe president of the southern Jubaland region, handing him back control of Kismayu.
But Somalia's central government, which does not view Madobe favourably, said his appointment was unconstitutional. Within days, three other men had pronounced themselves president, including Barre Hirale, a pro-Mogadishu former defence minister.
Despite the brief bouts of violence, fighting has so far failed to spread. The Somali government in Mogadishu, which has struggled to extend its influence beyond the capital, and regional players have all called for dialogue to end fighting.
But analysts say the chance of serious conflict increases the longer the stalemate over who rules the region continues. (Writing by Edmund Blair; Editing by Richard Lough and Andrew Heavens)