The Islamist group which controls much of southern Somalia has rejected accusations that it was behind the car bomb on the government base, Baidoa.
A government official has blamed al-Qaeda
Union of Islamic Courts (UIC) leader Sheik Hassan Dahir Aweys has condemned the attack, in which at least nine people died.
Government officials have accused the UIC of organising Thursday's blast.
There are fears of widespread conflict between the government and the UIC and their regional allies.
The government says they have arrested three more suspects following raids in houses and hotels in Baidoa, after three people were arrested on Thursday.
A government source says one of those arrested lost a leg in the explosion and another is a woman.
Police have tightened security around the town and several cars from the Islamist-held capital, Mogadishu, were not allowed to enter Baidoa.
A policeman told the BBC that a female suicide bomber wearing a veil blew herself up at a check-point on the outskirts of the only town under government control.
"There were flames everywhere," an eye-witness said.
Two of those killed were police officers.
The government says it was a suicide bombing but there is no independent verification of this.
"All indications are that they were trying to bring the explosives into Baidoa and their motive could be killing government officials, but we expect to get a clearer picture from the interrogation," Information Minister Ali Jama told the AFP news agency.
Some officials have suggested that the attackers were foreign members of the al-Qaeda network.
But Mr Aweys denied the charges.
"This is a baseless allegation. They have no evidence to say the Islamic courts are behind this," he told the AP news agency.
Interim President Abdullahi Yusuf survived a suicide car bomb attack in Baidoa two months ago, which killed his brother.
He said they were foreign members of al-Qaeda.
The UIC denies links to al-Qaeda but is opposed to the government and has threatened to launch a holy war to drive Ethiopian troops out of the country.
Ethiopia admits it has hundreds of military trainers helping the government but denies they are taking part in any conflict.
The Ethiopian parliament on Thursday passed a resolution authorising the government to take all necessary and legal steps against any invasion by UIC.
The resolution said there was a clear and present danger to Ethiopia from the UIC.
Ethiopia's rival Eritrea denies claims that it backs the UIC.