The forces armed with machine guns descended on the market forcing traders to hastily shut their businesses as they searched for illegal weapons awash in the seaside capital.
"They opened fire at everybody they saw moving around the market, three civilian were separately shot dead in the market.
"One was killed near my kiosk, he was a young man who used to exchange foreign currency and the other two were shot as they tried to inter the market during the operation," said Qoje Mohamed Ali.
Several witnesses confirmed the government forces used heavy-handed tactics.
The operation came a day after Islamic-led insurgents briefly took control of a junction near Bakara, where the government forces based during heavy fighting on Monday evening.
Somalia is increasingly running adrift since Ethiopia-backed forces ousted the Islamists early 2006 after months of fighting.
SOURCE: AFP, February 20, 2008