Several states in the deeply fragmented country are opposed to control by President Hassan Sheikh Mohamud, who also faces a long-running insurgency by the Islamist Al-Shabaab group that controls vast swathes of central Somalia.
In March, the government sent in troops to oust the head of South West State, Abdiaziz Hassan Mohamed Laftagareen.
He launched a failed attempt to retake the state in May, and in August his forces clashed with federal troops over control of the major city of Baidoa.
The latest fighting began around 4:00 am (0100 GMT) and lasted for several hours, with no immediate casualty figures available.
Somalia’s Ministry of Defence accused Laftagareen’s forces of having allied themselves with extremist Al-Shabaab insurgents to attack the city, a claim AFP was unable to independently verify.
“Somali Armed Forces defeated militias loyal to Abdiaziz Laftagareen and Al-Shabaab militants who had joined forces to attack Baidoa,” the ministry said in a statement.
They also claimed federal troops had “inflicted heavy losses on the attacking militias”, although AFP was unable to verify this.
A spokesperson for the pro-Laftagareen forces said they had captured parts of the city and that fighting was continuing.
However, several residents told AFP that Baidoa was now calm after six hours of clashes.
“The fighting was intense this morning,” said resident Hassan Mumin, who told AFP that forces loyal to Laftagareen had entered parts of the city before withdrawing, with the government now in control.
“I saw the bodies of two fighters,” he added.
Resident Mahdi Mohamed said while some areas remained calm, clashes in parts of the city reached by pro-Laftagareen forces were intense.
“Residents could not leave their homes until the fighting stopped,” he told AFP.
The ousted governor was among vocal opponents to the president’s attempts to move Somalia towards democratic elections, replacing a system based around clan elders.
But Mohamud has been criticised for extending his own mandate, while the security situation and divisions between rival clans mean there has been little progress on organising elections beyond a few localised pockets.
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