"Amara and Ba'adwayn are now under full control of al-Shabaab fighters," said a regional senior official who spoke on condition of anonymity.
Residents said al-Shabaab took the towns without resistance after local militias had fled. There were no Somali troops or African Union peacekeepers in the area.
Al-Shabaab already controls the port of Harardheere in the same region.
The group has staged several major attacks against AU troops in recent months, killing more than 90 peacekeepers in Lego and Janaale in the south.