At least seven people were killed in Burundi’s capital Bujumbura during a night of violence in flashpoint districts where months of protests took place against President Pierre Nkurunziza, police and witnesses said.

The deaths are the latest in a wave of violence convulsing Burundi which has raised fears the African nation may be sliding back into ethnic conflict after emerging in 2005 from a 12-year civil war.

Residents said police shot and killed five men in the Cibitoke district after house-to-house searches in the early hours of Wednesday, when gunfire could be heard echoing around Bujumbura.

Police spokesman Pierre Nkurikiye said police officers were responding to grenade attacks.

"The criminals threw three grenades at the police and our cops responded and killed five of them,” he said.

Nkurikiye said the administrative offices for Bujumbura city hall in another area were also attacked overnight by unknown men in police uniforms, leading to the deaths of a policeman and a civilian.

Civil society groups say more than 240 people have been killed since the unrest began in April after Nkurunziza said he would seek a third term in office. He won a disputed election in July.

"When (the police) arrived at the gates of those people killed, they forced the door open, took them out and beat them seriously before they ruthlessly shot them with many bullets,” said one Cibitoke resident who did not wish to be identified.