WADEBRIDGE School has boycotted the neighbouring leisure centre after demands that it should pay more than £40,000 a year to use it.
The school insists the sports hall at the complex was originally built for the benefit of its pupils and the wider community, and says it cannot afford the huge fee.
Wadebridge School became an academy last year, and now receives funding from central government instead of through Cornwall Council.
Because it opted out of local education authority control, the council and Carrick Leisure, the company which manages the centre, has told the school it now has to pay up to use its sports hall and changing rooms.
Head teacher Tina Yardley said the school felt it should not be charged to use the sports hall, and it would not be using any part of Wadebridge Leisure Centre again this summer, after negotiations over payment failed to reach a resolution.
She said the school considered the sports hall in the centre to be "ours".
In a letter to pupils, Miss Yardley said: "We have never had to pay to use our own sports hall, but we do pay to use the swimming pool, as this was added later.
"Things were still not resolved before the Easter holidays and we have had to make the decision not to use the sports centre at all this summer term while the meetings go on and the council decide what they might charge in the future. What we can't do at the moment is to carry on using it and then be asked for a very large sum of money that we just don't have.
"There's also the principle to be fought for."
The council said in a statement it was "disappointed" with Miss Yardley's comments in her letter to pupils "given that we are still in negotiation with the school to find a solution".
It said: "When the school transferred to academy status, it became responsible for its budgets, including the costs associated with using the leisure centre.
"All schools planning to transfer to academy status were made aware of the impact the transfer would have on their budget responsibilities," it said.
The school said in a statement: "The school is willing to contribute towards the running costs of the sports hall to reflect our use of these facilities, but the level of contribution has to be based on a realistic and fair figure that is affordable and, at this present moment in time, the council has not been able to provide this.
"The school cannot commit itself to an unknown and ongoing liability that would put significant pressure on the school budget that could lead to teacher redundancies and larger class sizes."