The school had already spent a substantial amount installing alarms in the classrooms and in the shed where the gear was stolen from, he said.
"That's big money that you are spending that comes out of the curriculum budget, that's the sad thing about it."
The school was a resource for the community and it was important it was open to the public, Mr Thompson said.
"This is a school that is a community school and we want our families that live here playing basketball and visiting our farm. If people come in and do that it's pretty sad and pretty hurtful - and pretty gutting for our caretaker in particular."
Although the front gate was often open, it had been locked at the time of the theft, he said.
Police had called in a police dog and handler to track the thieves, but the scent had died out near the Lighthouse Church where the thieves were believed to have got into a vehicle, Mr Thompson said.
It seemed the thieves had been quite organised, he said.
"I would suggest it's a group of people who knew what they were doing. The facilities were alarmed, but they didn't seem to be deterred."
It would cost about $10,000 to replace the stolen equipment and repair the shed and fence.
The quad bike was vital to the work caretaker Mike Clarke did and was used every day, Mr Thompson said.
Mr Clarke said as well as "taking money from the kids", the theft had put him behind on his work.
"It's just really, really, annoying. It's destroyed the day and all the plans I've had."
Anyone with information can contact Masterton police on 06 3700378, or call Crimestoppers anonymously on 0800 555 111.