Steve Kim Mission School, which is funded by a South Korean Christian, was accused of forcing Muslim children to convert to Christianity. Pupils of all faiths attend classes.
The incident is said to have took place earlier this month, but is only just coming to light.
World Watch Monitor says the attackers vandalised classrooms, destroyed the bakery and stole several items including computers and projectors. They also reportedly set fire to the library, burnt Bibles, hymnals and chairs; then cut the electricity lines of the school and destroyed a generator.
No students were harmed but it's believed 12 of the 14 staff members at the school were attacked.
Local police say 17 people have been arrested.