Fighting erupted between the town's pro-government rulers and the armed force of a local Islamic court.
Tension is high in central Somalia as the Union of Islamic Courts (UIC) that controls much of the southern end of the country, including the capital Mogadishu, tries to spread its influence further north.
The BBC's Hassan Barise says no one was injured during the short battle in the strategically important town of Beletuein, some 300km north of the capital.
The reason for the fighting is believed to have been related to a dispute over the administration's relationship with Ethiopia, he says.
The administration was appointed by the interim government based in Baidoa, which the local Islamic court accuses of being a puppet of Ethiopia.
The growing influence of the Islamic movement is in stark contrast to President Abdullahi Yusuf's 14-month-old transitional government.
Prime Minister Ali Mohamed Ghedi is attempting to form a new 31-member cabinet after it was dissolved last week.
Over the past fortnight some 40 ministers have quit their posts.
They resigned in protest at Prime Minister Ghedi’s opposition to peace talks with the UIC and he narrowly survived a parliamentary vote of no confidence.
The transitional government's weak authority is limited to Baidoa, a town 250km north-west of Mogadishu, and is supported by Ethiopia.
Somalia has been without an effective central government since warlords toppled dictator Mohamed Siad Barre in 1991.
The UIC has been credited with success in bringing stability to the capital, Mogadishu, for the first time in 15 years.