This species has a very localized and patchy distribution, but it can be relatively abundant where it occurs. It is threatened by habitat loss and conversion, although it seems to be fairly adaptable, and might thereby not be significantly threatened, except locally. Furthermore, caecilians often killed because they are mistaken for snakes. Ichthyophis mindanaoensis is known from Mount Kitanglad Natural Park, Malagos Watershed Area, and Mount Apo Natural Park, all relatively well protected and enforced areas.