The disagreement came during questions to education and employment junior minister Robin Squire, who was a guest speaker at the National Association of Grant-Maintained Primary Schools’ conference in Stratford-upon-Avon.

One teacher complained that anti-GM factions often divided parents at meetings called to debate whether a school should opt out. The parents often backed off, he said, which ended in an anti-GM vote in the ballot. But when he called for the ballot to be scrapped, there were cries of “rubbish”, “no” and “hear, hear”.

Mr Squire said he was “pleased to see there is such a good debate. I ask everyone of you to see there are these two sides. Every one of you knows one or two schools where the head wants to go GM but cannot face the thought of a parental ballot.” But another teacher in the audience said it was only thanks to parents at his school that it was GM at all - they had petitioned to opt out.

The current procedure for opting out involves a parental ballot only after the governors have voted on the issue. The Government is consulting on plans to scrap the parental ballot at church schools but the consultation paper also asks schools for their views on dispensing with parental ballots at all schools seeking to opt out.

Earlier Mr Squire had said some people would be unhappy if the parental ballot were suspended, but he asked how long should the country go on denying itself and schools the advantages of running themselves?

Afterwards, the association’s chairman, Bob Wright, headteacher of Bourne Abbey in Lincolnshire, the first primary school to go GM, said: “I think it is very important that parents do have a say . . . What is perfect for one school is absolutely disastrous for the next. We have to live with reality.”

However, he acknowledged that there were problems. Heads and governors often discussed the possibility of going GM for months, but parents had to make their minds up on the basis of comparatively little knowledge. And some governors dismissed the issue without discussing the pros and cons in depth, said Mr Wright.

The solution to the problem, he said, was for all schools to hold a parental ballot on GM every two years. A regular ballot would ensure that the issue was discussed in depth.

The National Association of Grant-Maintained Primary Schools has not yet submitted its formal response but Mr Wright said its reply would explain the advantages and disadvantages of the parental ballot.

Association members are also concerned about the difficulties of setting up new nurseries at GM schools and a national funding formula. One member from Essex said he was being “mugged” by the local education authority.

GM schools who wanted to set up nurseries were being “undercut” by the authorities and were unable to compete, he said.

And another member complained that GM schools were being “stitched up” by the authorities which tried to stop them getting planning permission for building projects.

Mr Squire said the logjam of GM nursery applications had now been cleared and warned LEAs that if they persisted with being obstructive then, in this area at least, their days were numbered.