Battles have raged across central and southern Somalia in recent weeks as Somali troops backed by the moderate Ahlu Sunna Waljamaca militia struggle to reclaim territory from al Shabaab, which has links to al Qaeda.
The soldiers captured Luq, 80 km (50 miles) from the Ethiopian border, and Elwaq, a frontier town close to Kenya after taking Beledhawo over the weekend.
"We have taken Luq town after a brief fight. Al Shabaab has fled," Abdi Fatah Mohamed Gesey, former governor for Bay region, told Reuters by phone from the agricultural town.
"We will not stop our operations against al Shabaab. The residents have warmly welcomed us and our next stop will be Baidoa."
President Sheikh Sharif Sheikh Ahmed said on Saturday his fighters were receiving logistical help from Ethiopian troops.
Sustained clashes over the past week have focused on the capital and Somalia's southern border with Kenya. Government troops and African Union peacekeepers say they have inflicted heavy losses on al Shabaab militants in Mogadishu
"Our troops have captured Elwaq, nine km from the Kenyan border, peacefully," Colonel Mahamud Ali Shire told Reuters by telephone.
"They run away from the town. We are now headed for Garbaharey, we have heard their last convoy has left for Bardhere to keep their foreign fighters safe, but we will not for a minute stop our fight against them."