Police said the searches were conducted by the dog squad and were carried out at the request of principals and local police out of school hours.
Teachers, parents and civil liberty campaigners said the practice breached students' rights.
"I think it is fairly invasive," said Beth Sheffield, president of the Victorian Federation of State School Parents' Clubs. "If they were adult institutions, would it be deemed appropriate for sniffer dogs to perhaps go through a department?" She said it could glamorise drug-taking among the students most at risk.