A spokesman for the African Union (AU) peace keeping force, AMISOM, said al Shabaab fighters had attacked them in one district late on Saturday, but that they and the government now controlled most of Mogadishu.
After al Shabaab started its withdrawal, President Sheikh Sharif Ahmed said his troops had defeated the rebels intent on overthrowing his Western-backed government.
Al Shabaab, which has its stronghold in the south of the anarchic country, denied this and said it would re-group and fight on.
Somalia has been without effective central government since the fall of dictator Mohamed Siad Barre 20 years ago, and is now suffering mass hunger from the worst drought in decades. Peace remains a distant prospect.
“Last night al Shabaab fired mortars and attacked us… they were not so strong, we chased them immediately,” an AMISOM spokesman, Captain Ndayiragije Come, told Reuters on Sunday.
“AMISOM and the government forces now control 90 percent of the capital. We are very sure we shall uproot the few al Shabaab elements remaining in the few parts of the capital.”
Residents said the fighting had continued into Sunday and that in some areas al Shabaab fighters had the upper hand