Somalia's al Shabaab group has taken control of El Bur, a town in the Horn of Africa's semi-autonomous region of Galmudug, after Ethiopian forces left, a government official has said.

Al Shabaab is seeking to drive the African Union-mandated peace keeping force, AMISOM, out of Somalia and topple the country's Western-backed central government.

The Islamist militants also want to rule the country according to a harsh version of sharia, or Islamic law.

"Ethiopian troops left the town ... thus al Shabaab captured it today," Burhaan Warsame, Galmudug’s minister for ports and sea transport, told Reuters late on Monday.

Ethiopian forces, who are part of AMISOM alongside troops from Uganda, Kenya and other countries, had captured the town from al Shabaab in 2014, officials from the area said.

Most residents fled into nearby bushland with the arrival of Ethiopian forces in El Bur, and Warsame said the town was deserted when al Shabaab fighters entered.

Al Shabaab has been driven out of its strongholds in Somalia by AMISOM and Somali army offensives, although the group still controls some rural areas and often launches guerrilla-style assaults and frequent bomb attacks in the capital, Mogadishu.

Sheikh Hassan Yaqub, al Shabaab’s governor for Galmudug's Galgadud region, where El Bur is located, confirmed the group had retaken the town.

"We captured it, there were no residents for over the three years Ethiopian troops controlled the town," he said.