About 30,000 people have been displaced following clashes between government forces and rebels in Burundi.
President Ndayizeye met FNL rebels in January
Army spokesman Adolphe Manirakiza said they have been fighting rebels from the Forces for National Liberation (FNL) south of the capital, Bujumbura.
About 25 rebels have reportedly been killed in the three-day military operation at the FNL stronghold.
Last year the government signed a peace deal with the main rebel group Forces for the Defence of Democracy (FDD).
About 300,000 civilians were killed in the 10 years of civil war in Burundi.
FNL rebels have refused to enter into a peace deal with the Burundi government.
Mr Manirakiza said the army had stepped up its operations in the rural province of Bujumbura.
"The FNL killed three civilians and wounded a fourth when they launched shells on the house of Kabezi's mayor," Mr Manirakiza told AFP news agency.
Correspondents say the fighting has now stopped.
FNL representatives met Burundi's President Domitien Ndayizeye in January for the first time.
Both parties agreed to end hostilities but the FNL has accused the government of not sticking to the agreement.