Hulme Hall currently charges £14,000 a year, but the fee is expected to rise after January, when the removal of the VAT exemption takes effect.
Tim Lowe, the chairperson of the school’s board of governors, said some parents will not be able to afford the increase.
He said there was a “big misconception” that private schools “are full of money like Eton and Harrow”.
He said the small trust which runs the school could “not cushion this extra money”, adding any surplus it generates goes back into the children’s education.
Mr Lowe described the VAT relief removal as “an education tax”, adding “most of that will have to go onto the fees”.
The Independent School’s Council estimates there are more than 6,000 pupils considered to have special educational needs in private schools in the north-west of England.
But more than two thirds of them would not qualify for extra support in the state sector, the body’s chief executive officer Julie Robinson said.
She said the VAT hike would “disrupt education for thousands of pupils”, adding she was “particularly concerned for what it might mean for students receiving SEND support”.
“A rushed January implementation will exacerbate these issues and we are calling on the government to at least delay implementation to allow VAT to come in in line with the academic year and school admissions cycles”, she added.
