The damage could cost the school up to $250,000, he said.
The cause of the blaze was not yet known, but a fire safety officer was investigating.
"It could be possibly connected to one or two break-ins we may have had during the night, but it's hard to know, it could have been anything," Mr Pannett said.
"They were redeveloping the block so the chances of an electrical fire were pretty high I imagine."
He said the damage would he disrupting for the school.
"We had anticipated having these two classrooms back in our possession at the start of the year - that's not going to be the case obviously and I guess they're going to be two terms, three terms away.
"So it's a massive inconvenience."
But Mr Pannett said it was a big school and they would be able to reshuffle classes and the timetable to accommodate.
"But thankfully, obviously there's no people involved."