No fewer than 20 houses were also allegedly burnt down in the attack.
Peri, near Potiskum, is the economic capital of Yobe State.
"A group of gunmen came into the village at midnight and went straight to the church. They opened fire on them (the worshippers) and then set fire to the church," said Usman Mansir, a resident of the village, according to Aljazeera online.
A senior police official in Yobe State also confirmed the incident to the AFP news agency, but declined to be named.
Yobe State Commissioner of Police Sanusi Rufa'i said the attack was "a security issue" and refused to comment further.
It was not clear who was behind the attack, but fighters belonging to the Boko Haram sect have carried out several attacks in the state and environs, which borders Maiduguri state where the activities of the group is most pronounced.