The controversial policy on gay students at Vanier Catholic Secondary School in Whitehorse is being thrown out immediately.
Education minister Scott Kent said the directive doesn't meet the department's requirements.
The Vanier policy follows the teachings of the Catholic Church on homosexuality, which views it as morally wrong. The policy has angered many parents, teachers and students.
Kent met Tuesday morning with Whitehorse bishop Gary Gordon on the issue. He said they both agreed the policy should come down.
Kent said a new set of guidelines will be made for the school, adding that the new directive will include input from parents and students, as well as from the Vanier school council.
Meanwhile, Kent said an incident where a former Vanier student was harassed is being investigated.
In that incident, a 16-year-old lesbian student had obscenities carved onto her school locker. She said principal Ed Frison minimized the incident and didn't take immediate action.
Kent said the department's human resources staff is dealing with the issue.