The killings Monday night occurred in the southeastern province of Makabma in this central African republic.
The Hutu rebels, of the Forces for the Defense of Democracy, attacked the church, near a military center, where some 100 residents of Nkondo had sought refuge.
Bloody conflicts between the ruling Tutsis and rebel Hutus have scarred Burundi since 1993. A peace pact signed a year ago has failed to stop the fighting.
