Urbain Kabore, the communications director for the Sahel region of Burkina Faso, said Monday that the six people were killed after Sunday services.
There was no immediate claim of responsibility.
Violent Islamist extremism has been increasingly destabilizing Burkina Faso, and a number of jihadist groups are known to operate in the area of the attack.
Authorities said that in a separate attack in the east of Burkina Faso, five teachers were shot to death Friday.
The extremists also have targeted foreigners, abducting and killing a Canadian geologist earlier this year.