Council chief executive Ross McNeil said it was a significant cost.
Work needed on the building included meeting fire safety requirements and repairing broken windows and guttering.
The grounds were also in need of a tidy up, while there was a large area which would need year-round mowing.
Last week councillors gave Mr McNeil the green light to meet the ministry to discuss terms. He will push for a deal that could include less responsibility for the council and cost sharing with the ministry.
Councillor Dean McManaway said the council should try to recoup as much of the running costs as possible from users and consider leasing some of the land.
"I first looked at that and thought 'good'. But that's a considerable amount of money," he said.
At present nine groups are using facilities at the school, but seven are community groups and Mr McNeil said that meant recovering costs was unlikely.
Mayor Andy Watson said there were several options, including not entering an agreement with the ministry, but he also said both current user groups had invested a lot into the school property.