The principal was checking the building on Friday ahead of the coming school holidays when she discovered the plants in a locked area.
Besides the principal, the accused was the only person to have the key.
Police say only a small amount of cannabis was being produced on a plantation measuring three by three metres.
But they say the site was "spectacular" and was complete with lighting, irrigation, heating and ventilation.
The accused worker, 35, says he was growing cannabis at the school for his personal use.
Police have placed him on probation awaiting an appearance in court.