A Fire and Emergency New Zealand spokesman said they received reports of a fire at the Coptic Orthodox Catholic Church of the Archangel Michael in Melville St at 9.25am.
Units from Dunedin City and Willowbank responded, and an aerial appliance was also dispatched.
A "small fire" was soon extinguished.
The fire was being treated as suspicious, the Fenz spokesman said.
An investigation is under way.