Education Secretary Gillian Shephard is currently considering requests from Bennett Memorial Diocesan School in Tunbridge Wells and Droxford primary near Southampton that their opt-out applications be torn up.
The proposals can only be withdrawn with the Education Secretary's consent and she will now either have to force the schools to opt out against their will or allow them to drop their proposals at a time when interest in opting out is at an embarrassingly low level.
Despite claiming last month that interest was "getting stronger," only 13 English secondary schools voted to opt out in the past 12 months while no Welsh school has voted to opt out since July 1993.
The position in the primary sector has also showed a marked decline with only 27 of the 20,000 schools in England and Wales becoming grant-maintained in the past year.
Bennett Memorial - a 1,100 pupil C of E comprehensive - wants to withdraw its application in a dispute with ministers over its admissions.
The school has objected to Government demands that a long-standing arrangement under which parents accepting a place commit themselves to comprehensive education by withdrawing their children from the 11-plus selection procedures elsewhere in the county is changed. Rosalind Plumley, chair of governors, said governors unanimously believed that the character and ethos of Bennett as a C of E comprehensive was "indissolubly" linked to the present admission procedures.
The governors' stance is backed by more than 800 parents at the school where support for GMS was overwhelming and where there are two pupils for every place.
"We have pointed out to the Secretary of State that her department at no time indicated to us while we were considering GM status that it might be granted only on conditions which we could not accept," said Mrs Plumley.
"To forfeit these arrangements, we believe, would be to endanger the school. We now believe that the future of Bennett will be more effectively safeguarded if we remain an aided school, within the voluntary system."
Kent County Council has given an undertaking that it would support the present admission procedures were Bennett to remain with the local authority.
A spokeswoman for Kent said: "We would welcome Bennett Memorial's return to working within the local education authority partnership."
Droxford - with just 59 pupils - applied to opt out when it was threatened with closure under a rationalisation of primary places in Hampshire. It was reprieved by the local authority to become a junior school and a spokeswoman said: "The decision came after consultation and a big campaign against closure ."
Ministers have insisted that opting out would not be an escape route for schools threatened with closure. Only 58 of the 1,049 GM schools in existence were either facing closure or re-organisation.
The Department for Education said that the two proposals, believed to be the first withdrawals on GMS in the country, were under consideration.
Martin Rogers from Local Schools Information said: "Bennett is a classic illustration that GM schools are not self governing.
They are obliged to do what the Secretary of State tells them. While Droxford just shows that people shouldn't jump the gun.
"The question now is, is the Government going to force people to opt out who don't want to?"