The proposals, which would create three new classes of school, have been condemned by Local Schools Information, an organisation backed by local authorities.
In 48,000 leaflets to be sent to schools and local authorities this month, LSI has warned of a repetition of "divisive" campaigns and ballots and the creation of a GM sector in exile.
LSI, which has been involved in about 800 opting-out meetings in the past 10 years, spoke out as ministers consulted on proposals for a new framework of "community", "aided" and "foundation" schools which will form part of an Education Bill this autumn.
It said the new structure had not appeared in Labour's manifesto and that there had been little debate since the scheme was unveiled in a policy document two years ago.
"Due recognition must be given to the extent to which structural issues have the potential to undermine the standards agenda; they cannot simply be wished - or willed - away," it said.
LSI's criticisms follow condemnation of the proposals earlier this month by the Anglican and Roman Catholic churches, who were united in warning of the end of the church school system.
Ministers expect county schools to take on community status and church schools to become aided while GM schools opt for the foundation category. However, some church GM schools have already said they will become foundation.
All schools will be provisionally allocated to what the Department for Education and Employment believes to be the closest and most appropriate category.
LSI said: "The fact that foundation schools would be seen largely as the GM sector in exile already appears to have provoked widespread antipathy towards the concept of foundation status among the large majority of schools which, despite the financial and other inducements, chose for years to remain LEA-maintained, as a matter of principle.
"Nevertheless, if faced with the prospect of many of their neighbours becoming foundation, county schools could feel pressured to move to foundation status rather than community status - raising the prospect of a repetition of divisive campaigns and ballots."
The organisation proposes that the Government should introduce just two new categories of school - community and voluntary - scrapping plans for a foundation sector.
Community schools would be those provided from public funds. The LEA would own the premises, employ the staff and act as the admissions authority.
Voluntary schools would be all those whose premises were provided on a voluntary basis and vested in a trust separate from the governing body. Premises would be held in trust, staff employed by their governing body or by the LEA - while admissions would be looked after by governors or the LEA.
Both categories could have a significant number of co-opted governors while voluntary denominational schools could have seven foundation governors.
It claimed such a move would "leave people free to focus on standards without the distraction of further structural considerations".