The casualties were from both sides in the fighting, the defence officials said.
According to the first official toll from the fighting in the morning, eleven rebels and one loyalist soldier were killed and two governmental soldiers seriously wounded.
By Wednesday afternoon, sporadic shootings were still being heard several kilometres away in the mountains overlooking the capital.
The Defence ministry said the fighting started when the regular army undertook to flush out elements of the rebel National Liberation Front (FNL) who had laid an ambush.
The clashes occurred in Mubimbi and Mageyo, two communes in Rural Bujumbura.
Bujumbura Mayor Pontien Niyongabo has alleged the FNL troops were planning other attacks on the Burundian capital.
- Pan African News Agency
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