Sunday's fire at Kerikeri High School will keep the school closed for the next two days.
Principal Elizabeth Forgie says a physics classroom has been destroyed and three other rooms are likely to be condemned and demolished.
Police say a fire was lit deliberately beneath benches outside a classroom early on Sunday morning. They are examining footage from the school's security cameras.
Ms Forgie says the clean-up involves removing chemical residues from the destroyed science lab and fixing electricity and water supplies, but a new timetable will be drawn up and all 1400 pupils should be ready to return to school on Thursday morning.