The AU on Friday denied on Friday it has lost control of Merca, saying it had made a tactical withdrawal.
Al-Shabab was forced out of the capital Mogadishu in 2011 but still has a presence in large areas of the south.
A Somali military official told AFP news agency: "The Somali forces and Amisom [AU] peacekeepers secured control of Merca again and now the situation has returned to normal.
"There was brief exchange of gunfire, but the militants have fled."
He said "several" al-Shabab fighters and one Somali soldier had been killed in the fighting. A resident told AFP that four civilians had died in his area.
The fighting comes three weeks after al-Shabab overran an AU military base outside the southern Somali town of el-Ade, saying they had killed about 100 Kenyans soldiers.
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