In a Monday statement, AMISOM head Maman Sidikou said that Al-Shabaab militants now only control Jamaame, Jilib, Buale and Sakow in Middle Juba Region, Diinsor in Bay region and Bardere in Gedo region.
"There are also a few other smaller towns like El-Dere in Middle Shabelle," he added.
Sidikou earlier met with Somalia President Hassan Sheikh Mohamud, senior army officers and AMISOM before giving a briefing on "Operation Indian Ocean".
The AMISOM head, meanwhile, said that security in Somali capital Mogadishu has improved.
"Let me assure our Somali brothers and sisters that…we will not leave any stone unturned in the fight against Al-Shabaab," Sidikou said.
"We are confident that, working together, we will overcome the Al-Shabaab menace."
The Somali president, for his part, said that Al-Shabaab militants have been battered.
"Al-Shabaab has been battered relentlessly and has lost much in terms of men, equipment, weapons and criminal funding opportunities," Mohamud, who last week visited the recently captured Barawe port, said.
"But it has not been annihilated. It has scuttled off and is now hiding in dark areas, out of sight for the moment, but desperate to reassert itself," he added.
"The fall of Barawe marks a turning point in the fight against Al-Shabaab. Barawe was Al-Shabaab's last major stronghold," he noted.
For years, the Al-Qaeda-linked Al-Shabaab group has been fighting the central government in Mogadishu and African Union-led peacekeeping forces.
A long-troubled country in the Horn of Africa, Somalia has remained in the grip of on-again, off-again violence since the outbreak of civil war in 1991.