While the gym and technology blocks are set for a rebuild, the process has been "glacially slow", he said.
Unsurprisingly, the school had one of the highest rates of vandalism in Northland costing hundreds of thousands each year. The kids were using their anger to lash out on their environment, Mr Paitai said.
Despite the mouldy classrooms, student NCEA results were good, he said.
Image 1 of 9: Bay of Islands College principal John Paitai points to the gym mezzanine which is not open because of the rotten floor. Photo / Jessica Roden
For example, 76.3 per cent of students achieved Level 2 last year.
"It's not an excuse for us not being able to achieve with our students," Mr Paitai said.
The technology block, built in the 1940s, contained a room with black mould growing from the ceiling and covered in condensation constantly. It was sealed off from students. One of the teachers, who put his foot through the rotten floor twice, sat at a desk with black mould growing above him. Mr Paitai said he was "embarrassed" by the block.
Leaky roofs were an issue throughout the school, he said. For example, 12 classrooms were without power last Friday morning after a water leak caused an outage.
Ministry of Education head of education infrastructure service Kim Shannon said it was working to finalise a plan which would see the classrooms with toxic mould demolished and replaced with a new technology block.
The ministry had recently agreed to fund a $1.8 million rebuild of the gym, Ms Shannon said. Staff and students were forbidden from going up to the mezzanine of the gym because the rotten floor was a safety hazard. The school had $1.4 million available to put towards buildings. $641,000 remained from a grant five years ago and it was today given $766,000 for the next five years, she said.
"We're concerned to learn about some of the issues the school says it is facing and we are talking to them about why they haven't accessed the funding that is available to address those issues," Ms Shannon said.
Mr Paitai said he was hesitant to answer about issues before his time. "Why they did not do it five years ago I would not know," he said.
While waiting for the rebuilds it was "common sense" to be careful with the money, Mr Paitai said. "We don't want our precious money wasted on fixing this when it's going to be knocked down again."
He said the school was saving the money to refit the new technology block and upgrade areas not part of the rebuild. Maintenance was constant with professional cleaners regularly visiting, Mr Paitai said.
The revelation of the school's building woes come a month after Northland College principal Jim Luders labelled his school's classrooms the "worst in New Zealand".