A militia previously allied to the Somali government in its fight against militant group al Shabaab has captured two towns in central Somalia from federal forces, saying it was taking control where the government had failed to end the insurgency.

On Thursday, Somali federal forces attacked the Ahlu Sunnah Wal Jama'a (ASWJ) militia in Galmudug state, culminating in fighting that saw its troops ousted from the towns of Mataban and Guriceel, spokespeople for both ASWJ and the Somali National Army (SNA) told Reuters.

The army accused the ASWJ of planning to attack its troops, which the group denied.

"Yesterday, we attacked ASWJ... because we knew they were planning to attack us," Captain Nur Abdullahi, an officer for the SNA told Reuters from the Galmudug capital.

Sheikh Ismail Farah, a spokesman for ASWJ, said the group had had no such plans and did not want to fight the government.

"We are ready to eliminate al Shabaab. Al Shabaab is our common enemy," he said.

The group has not denied the army's accusation that ASWJ fighters had been fighting al Shabaab unilaterally.