Devote Ndayizeye, the administrator of Gatara commune in the province of Kayanza where the attack took place last night, said two of the victims died of their wounds after being hospitalised.
Ndayizeye said the attackers fled the scene and their motive remains unclear.
Burundi has been plagued by sporadic violence since April 2015 when President Pierre Nkurunziza's decision to seek a third term led to street protests.
Nkurunziza won another term in disputed elections in July 2015 and remains in power, but Burundi has stayed unsettled. At least one armed group has announced a rebellion and sporadic violent attacks has sparked fears of a return to civil war.