On Saturday, Abdirahman Nur Mohamed Dinari, the government spokesman, said about 300 military men were brought to dismantle checkpoints in Baidoa which were being set up by "a few individuals and gunmen".
He said: "When they accomplish the dismantling of the checkpoints they will immediately hand over to the police in Baidoa."
But residents said as many as 1,500 troops had arrived in the town, where the largely powerless government has set up camp owing to insecurity in the bullet-scarred capital Mogadishu that has been the scene of fierce battles in recent months.
The town was largely peaceful on Saturday after the clashes that were sparked when the government decided to help local authorities in Baidoa and five surrounding districts clear illegal roadblocks, where armed men extort money from civilians, and to disarm freelance and clan militias.
Clashes at such checkpoints are common among lawless Somalia's many armed groups, for whom the barricades are a major source of income.
"The whole task of the presence of the force in Baidoa is to bring peace, nothing more, nothing less," Dinari said.
Friday's fighting involved soldiers loyal to transitional president Abdullahi Yusuf Ahmed Yusuf - coming mainly from his home region of Puntland in the north - and armed men from a militia controlled by the Raharwein clan, which is dominant around Baidoa, witnesses said.
Tension has gripped the nation
since Islamists seized control
The presence of Yusuf's troops has heightened tensions in the town, with local militias complaining that fighters from northern Somalia are taking their jobs and income.
On Saturday, the government was meeting to discuss ways of establishing a permanent security force in Baidoa, according to a minister in Yusuf's government who spoke on conditions of anonymity.
Ehab al-Alfi, Aljazeera's correspondent in Somalia, confirmed from Mogadishu that intensive negotiations between government officials and leaders of local tribes and armed factions followed Friday's deadly clashes in Baidoa.
Islamist militiamen shot in the air to disperse hundreds of Somalis protesting early on Saturday against moves by Sharia courts to stop them from watching the World Cup in the capital Mogadishu, residents said.
The football tournament had drawn huge crowds to TV screens set up under trees and iron-sheeted shacks, providing some escape from the tension that has gripped Mogadishu since Islamists seized control from an alliance of secular commanders on Monday.
Witnesses said scores of young men set fire to tyres late on Friday in protests that carried on into the early hours of Saturday after Islamist militias pulled the plug on makeshift cinemas airing the World Cup.
Two people were wounded when militias tried to break up the demonstrations that centred around the main livestock market in an Islamist stronghold in the capital's north, residents said.