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Principal Ronan Bass said the burglars broke into to the canteen with a crowbar.
"They have then stolen the cash register and unfortunately all of the freezer lids were left open overnight so the food has now spoiled and is unable to be sold," he said.
Mr Bass said the canteen is operated by a private company. As a result of the break-in, the canteen will be closed for the rest of the school year.
"Obviously this has created quite a dent in their profit margins so the decision was made to close it for the remainder of the year."
He said police have completed a scene examination and will continue to investigate.
"They have been out here today and really it's up to them now to work through the processes that they work through."