They will be forced to consider severing historic links with the church but will be unable to fit comfortably into Labour's new framework of foundation, aided and community schools.
In two years' time ministers expect the 2,715 voluntary-controlled schools in England to take on foundation status - the category also intended for former GM schools. Foundation schools would own the land and buildings and the governors would employ staff.
The problem this poses is epitomised by a 290-pupil primary in Wiltshire. St Michael's in Melksham does not want to become a foundation school as it is opposed to opting out.
Unlike the three other primary schools in Melksham it refused to opt out on moral grounds.
It says its county council cannot afford to buy its buildings which would enable it to become a community (local authority) school and anyway it is reluctant to break its 157-year-old link with the Church of England.
Aided status is out of the question because St Michael's parents could not raise the 15 per cent contribution an aided school has to make towards capital and maintenance work.
"This proposed lack of choice makes us feel very angry," said Julia Oulton, chair of governors.
The school believes that the GM sector prevented local authority from providing a coherent and effective education for all children.
"It seems ironic that having decided not to become a GM school for reasons of wanting to remain a community school and a belief in equality, St Michael's will have to become a foundation school under a Labour government," said Mrs Oulton.
"Meanwhile, we will have missed the chance of the extra resources GM schools have had."
Headteacher Stephen Bicknell wants his school to remain voluntary controlled within the community. He said: "Only as a last resort would we wish to become a community school and break our historic link with the Church."