Police began exhuming bodies on Friday, said Charles Kamau, a detective in the nearby town of Malindi, without giving further details.
The leader of the church, Paul Mackenzie, was arrested following a tip-off that also suggested the existence of shallow graves belonging to at least 31 of Mackenzie's followers.
Police said the 15 rescued worshippers had been told to starve themselves to death so they could meet their creator.
Matthew Shipeta from Haki Africa, a human rights group, said he had seen at least 15 shallow graves in the forest.
"Personally I have visited about 18 children's graves," Mikali told Citizen TV.