Gunmen have attacked the compound of Somalia's interim President Abdullahi Yusuf in the central town of Baidoa.
Gunmen have controlled Mogadishu for 15 years
At least 10 people were killed in heavy fighting when a local clan militia attacked the area reportedly angry at moves to dismantle their roadblocks.
The unrest comes as the government discussed a response to the Islamist victory this week in the capital.
Militia of the Islamic courts seized Mogadishu from warlords, who had controlled the city for some 15 years.
The central town of Baidoa, some 200km from Mogadishu, is the temporary base of President's Yusuf's fledgling administration, which has not moved to Mogadishu because of security concerns.
There are some 3,000 militiamen operating in Baidoa who extort payment from the scores of checkpoints that line the route to Mogadishu.
The BBC's Hassan Barise in Mogadishu says the gun battles broke out in the centre of Baidoa on Friday morning.
Among the dead included a well-known leader of the Geledleh clan, Malaq Somow Abdi Garrun, whose militia led the attack. MP Mohamed Hussein Afaraleh was among the wounded.
President Yusuf was in his compound at the time of the fighting.
Our correspondent says the battle may have been a sparked by an attempt by the president's militia to disband an illegal roadblock set up by local Geledleh militia on a road into Baidoa.
In retaliation, the clan militias attacked the presidential compound, which is heavily guarded, our correspondent says.
The fighting forced all business in the town to come to a halt.
The building which houses the parliament is only 200m from the presidential compound and clan elders and MPs attempted to intervene to calm the situation.
By the afternoon the fighting had eased, with only sporadic gunshots being heard in the area.
Correspondents say although the clashes appear to be unrelated to the fighting in Mogadishu, they add to the heightened sense of tension in southern Somalia and the killing of a clan elder could see an escalation of the violence in Baidoa.
Ministers and MPs in the town have been discussing their response this week to the change of power in Mogadishu.
On Wednesday, a senior interim minister said he expected the Union of Islamic Courts to eventually join them in government.
The deputy head of the government, Ismail Mahmoud, said contacts had been taking place.
BBC Somali Service editor Yusuf Garaad Omar says the Islamists are generally more popular than the warlords, who are hated for their role in Somalia's civil war.
The transitional government only controls a small part of Somalia, which has not had a functioning national authority for 15 years.