The Transitional Federal Government (TFG), backed by African Union peacekeepers, controls only a small portion of the capital.
Similar clashes - between armed opposition groups on one side, and the government and AU on the other - happen on almost a daily basis, often resulting in civilian casualties.
An internal AU report disclosed last week called for "urgent attention" to the problem of civilian casualties, warning that the peacekeeping force risks losing public support in Somalia.
At an African Union summit in Kampala this week, the organisation decided to send another 4,000 soldiers to Somalia to bolster the roughly 6,000-man force.
Somali officials on Wednesday praised that decision, calling it a "lifeline" for their government.
"We applaud the fresh troop infusions made by AU states," Abdulkadir Mohamoud Walayo, a spokesman for the government, said.
"We believe this decision will help improve the security situation in Somalia, and also contain the threat al-Qaeda elements are posing to the region in general."