Duty lawyer Lisa Ebbers sought name and detail suppression, which was not contested by police prosecutor Grace Collett.
Judge Lawson granted the application and remanded the man in custody to reappear via audio visual link on September 21.
Eastern Bay of Plenty police arrested the man yesterday.
A fire at the school in the early hours of February 6 destroyed the office block and eight attached classrooms.
Today in a media release, Apanui School principal Simon Akroyd thanked the police for their work as well as all who supported the school in the wake of the fire.
He said the school board, staff, children and community were grateful for the commitment shown to their school.
"We would like to express our appreciation to the New Zealand Police for their dedicated work in investigating and making the arrest of a person in relation to the arson of Apanui School.
"Our school was devastated by the fire that occurred earlier this year on Waitangi Day. We lost eight classrooms, our administration block and several other buildings.
"Our community (locally and nationally) rallied around us incredibly. We've grown in the last six months, ensuring that our children and staff have been at the centre of our focus.
"We're currently operating with 10 classes on the school site that were not affected by the fire and with another nine classes on a temporary site, which borders our school."
Akroyd said the board was working with the Ministry of Education to rebuild lost spaces.
"The timeline is to have our children in their new classrooms at the start of 2023 and to have our administration block open from the start of term two, 2023.
"This arrest does not change what happened. It will not affect our day-to-day operation and what school is like for our wonderful children. It's simply another step in our healing.
"Our sincere thanks to the NZ Police for their determined work, communication, support and for their amazing resilience."
Akroyd highlighted the relevance of the school whakatauki; He manu hou ahau, he pi ka rere - I am a small bird poised for flight.
"Our community is resilient and we're poised for the new challenges ahead of us."