Several Somali traders have been arrested by Islamist militiamen after a protest over new taxes, in which one person was shot dead.
About 100 people staged the protest in the town of Jowhar, captured by the Union of Islamic Courts last month.
Meanwhile, a Djibouti minister has reportedly said that the US would not be allowed to use its base there to attack Somalia's Islamists.
The US accuses the UIC of having links to al-Qaeda, which they deny.
Djibouti Foreign Minister Mahmud Yusuf told the London-based al-Sharq al-Awsat newspaper that Djibouti would not be a staging-post for attacks on Somalia.
The United States set up an anti-terror base in Djibouti following the 9/11 attacks in 2001.
It was widely believed to have supported an alliance of warlords defeated by the Islamists in the capital, Mogadishu, last month.
US officials neither confirm nor deny the accusations but say they do not want Somalia to become "a safe-haven for terrorists", now that the Islamists control significant parts of the south of the country.
One of the members of the warlord Anti-Terror Alliance has gone to Baidoa, where the weak, UN-backed government is based.
Abdi Qeybdid has held talks with interim President Abdullahi Yusuf after being driven out of his Mogadishu base on Monday.
The UIC and the government are due to have peace talks in Khartoum on Saturday but the latest fighting has reduced the prospects of an agreement, correspondents say.
The government has accused the UIC of breaking the ceasefire deal agreed at the first round of talks.
In Jowhar, about 40 young men with plastic bags to collect cash began levying the taxes on the orders of the Islamist administration, reports Reuters news agency.
"I am not in a position to pay the taxes. Whatever I get from my small business, I feed my family with," said trader Fatuma Ahmed, mother of three.
She had been asked to pay 2,000 shillings (14 US cents).
The UIC has been consolidating its grip of the capital, by taking control of the port on Wednesday.
Mogadishu's main port had been closed for the last 15 years, because rival factions failed to agree who should run it.
One week ago the city's main airport was handed to the Islamic courts by militia who previously dug up the runway to resell cheap gravel for other construction work.