"We call upon civilians in Bakara to move from that area because we will go after the insurgents in that area," Habeb said.
Meanwhile, local media reported that at least 15 other people had been killed in fighting in the last two days, including as many as seven Ethiopian soldiers.
Dozens of civilians were also wounded by stray bullets and shrapnel.
"They have started firing again and I have no way to move my family," said Sahra Osman, a widow with five children.
"I have been fleeing my home and returning since the Ethiopian troops arrived here, but now I can't even hire a wheelbarrow."
Violence began before dawn on Saturday, with witnesses saying fighters exchanged machine-gun and mortar fire with government and Ethiopian troops.
Elmi Hussein, a Mogadishu man whose cousin died in Saturday's battles, said it was better to be killed outright than to suffer the fate of the injured in the Somali capital.
"The wounded die painfully here," he said.
"The roads to the hospitals are always blocked whenever war starts and people die from loss of blood."
The fragile Somali government has been beset by roadside bombings, assassinations and suicide attacks since it routed Islamic Courts fighters in January with the help of Ethiopian tanks and warplanes.
The new battles come as tensions at the top of the fledgling administration threaten a split.
Analysts say tensions between Abdullahi Yusuf, the Somali president, and Ali Mohamed Gedi, the prime minister, have been simmering since they came to power in late 2004.
The rift has widened in recent months as each has backed rival concerns hoping to exploit the nation's potential oil resources.