Some 30,000 people have fled their homes after reports of renewed fighting near the Burundi capital Bujumbura, officials say.
Burundians have suffered 11 years of civil war
A third of the residents of Kabezi district south of Bujumbura are reported to have fled.
A BBC correspondent says that some have sought refuge in a church but others are stranded in the region's hills.
The largest rebel groups have signed peace deals but one ethnic Hutu group continues to fight.
Rebels from the Forces for National Liberation (FNL) have refused to enter into a peace deal with the Burundi government.
They insist on negotiating with the Tutsi-dominated army, which they say holds real power, rather than the government led by President Domitien Ndayizeye, a Hutu.
FLN spokesman Pasteur Habimana says the FNL were defending themselves against both the army and fighters from the Forces for the Defence of Democracy (FDD) former rebels, which signed a peace deal last year.
Since the latest fighting began on Tuesday, nine rebel soldiers have been killed while a vast array of weapons were seized, according to Burundi army spokesman Major Adolphe Manirakiza.
Burundi's civil war began in 1993, when the country's first Hutu President, Melchior Ndadaye, was assassinated by Tutsi paratroopers.