The town of Garbaharey, located in the western region of Gedo and near the borders with Ethiopia and Kenya, had been under Shebab control since 2009.
"Our forces are now fully in control of Garbaharey town, which the Al Qaeda elements emptied this morning as we approached," Mohamed Abdi Kalil, the governor of Gedo region, told AFP.
"We will continue to advance on the other towns and, God willing, we will flush them out completely," he said.
Garbaharey is the latest in a string of major towns in the region the Shebab have lost in recent weeks, as pro-government forces continue their reconquest of large areas which had been under Shebab control for two to three years.
"The government forces entered the town around midday after the Shebab militants withdrew without fighting. I saw dozens of armed vehicles patrolling in the streets," Abdullahi Haji Mohamed, a local resident, said.
Shebab officials could not immediately be reached for comment but security sources in the areas said the Islamist fighters had temporarily retreated to around 15 kilometres (10 miles) outside the town.Continued