The Funding Agency for Schools - the quango which oversees GM finance - has just agreed an overdraft for Kirkby Stephen grammar in Cumbria, which opted out more than two years ago.
The school has been given three years to clear the debt. Peter Hawksworth, its headteacher, said: "There is some evidence that we might have been better off if we had stayed with the local authority - Pounds 15,000 better off - but it is very difficult to say."
David Garrick, vice-chair of its governing body, added: "A principal reason for going grant-maintained was the belief, misplaced as it turns out, that greater autonomy would lead to increased flexibility over spending priorities.
"We now have insufficient funds to meet our statutory curriculum obligation in an acceptable way, let alone those essential additional responsibilities which fall on GM schools."
Their revelations will be profoundly embarrassing for the Conservative party during its conference week and particularly for the Prime Minister who is pushing for all schools to go GM.
Ministers have been keen to extol the flexibility that total control of their budget gives to GM schools.
Kirkby Stephen, a 336-pupil school, has lost money through the Common Funding Formula, the funding system which covers GM schools and which has just been introduced in Cumbria.
Under previous GM arrangements it received Pounds 722,169, including Pounds 50,502 to compensate for loss of central services and Pounds 7,150 in school meals grant. Now it gets Pounds 707,169.
The county council gave it Pounds 664,499 through local management and although it has no breakdown for what it spends on central services and meals grants for individual schools, David Johnston, its financial controller, said the authority would have spent in excess of Pounds 50,502 on central services.
Headteachers now predict that at least three-quarters of the schools in Cumbria - including GM schools - will overspend this year.
The local authority said that 60 per cent of its schools went into the red in 1994-95, while 41 per cent are forecast to do the same this year.
Kirkby Stephen did not set a budget this year. It has been affected by a 4 per cent reduction in secondary pupil funding in Cumbria as well as the county's and Government's refusal to fund fully the teachers' pay award.
It has lost two teachers and had to remodel its curriculum at key stages 3 and 4 from three groups to two.
"Ironically," said Mr Garrick, "all this occurs during a period of capital investment at Kirkby Stephen (approximately Pounds 300,000) as a result of successful ring-fenced grant applications.
"This really does expose the shambles of current funding arrangements with a real possibility of refurbished facilities but not teachers."