Somali Prime Minister Ali Mohammed Ghedi has appealed for an end to fighting in the town of Baidoa which has left at least 14 people dead.
Speaking from Libya, he urged the rival militias to observe a ceasefire following two days of clashes.
There are fears the fighting has damaged hopes of an immediate return for the government exiled in Kenya.
On Monday there was a lull in fighting between militias loyal to rival Somali warlords - both of whom are MPs. The clash began over whether the exiled government should be located in Baidoa.
Last week, MPs backed a proposal that the government should be based not in the capital, Mogadishu, but in Baidoa and Jowhar and there were celebrations to mark this decision in Baidoa on Saturday. However, one powerful warlord apparently ordered his troops to attack those who were out on the streets and a fierce gun battle broke out.
Baidoa is now in the hands of the militia led by Mohamed Ibrahim Habsadeh.
The militia commanded by Hassan Mohamed Nur Shargudud is reported to have left the town.
A BBC correspondent in the region says this latest round of fighting makes it appear unlikely that the interim government will be going back to Somalia from the Kenyan capital soon.
Meanwhile, a group of nine Somali MPs from Nairobi have arrived in Mogadishu on Sunday to assess the security situation.
Somalia has not had a functioning government for 14 years and has been divided by rival warlords.
East African countries have agreed to send some 6,800 Sudanese and Ugandan troops to Somalia to aid the government's return but several Mogadishu-based warlords oppose the use of foreign troops.
MPs were involved in a brawl during a debate on the issue last week.