Six out of 10 grant-maintained secondaries will lose staff when their sector is abolished, according to the results of the TES survey.
More than 500 jobs - at least half of them teachers' - are thought to be at risk.
Secondary schools, which account for 56 per cent of the GM sector nationally, will bear the brunt of the job losses. Some headteachers told The TES that they were preparing for staff cuts in double figures.
Just over 50 heads (19 per cent) did not expect to lose staff and 61 (21 per cent) did not know what would happen.
More than a quarter of the 285 secondary heads responding to the survey said that GM status had enabled them to take on extra teachers, classroom assistants and adminstrative support.
But for one at least the writing has been on the wall for a couple of years.
The head of a technology college said: "We did receive favourable treatment which was perhaps unfair. In the early stages we did very well, but in the past two years the party seemed to be over."
The majority of GM secondary schools replying (263, or 92 per cent) said they would opt for the Government's new foundation status - the nearest equivalent of GMS but which does give local authorities a say.
Heads warned LEAs that they had plenty to fear from the GM sector. "We are unlikely to tolerate poor services, interference or ineptness," said one Surrey head.
While the head of a technology college said: "I do not expect to have to put up with the third-rate services offered to me previously. I do not want interference from LEA inspectors or advisers. I will seek advice as I have done for the past four glorious years."
Overall, 45 per cent expected trouble with their former authority, 40 per cent did not, 11 per cent were unsure and 4 per cent did not answer.
The head of a Derby community school said:"I'm sure that there will be an attempt to 'teach those GM schools a lesson'." While another county head added: "Why would Derbyshire change the habits of a lifetime?" In Birmingham a head reported the authority had always been aggressive and bitter - "Tim Brighouse, the chief education officer excepted" - but added:"We are not frightened. "
Many were bullish. The head of a Midlands secondary said: "We have learned too much and cannot "un-know" what we now know." And the head of a Kent secondary school said: "Why the Government should want to damage or destroy the advances made by 1,100 GM schools is beyond me."
There was also concern. The head of a technology college, which opted out because of poor funding, said: "I am very concerned that the Labour government (for whom I voted) says it is putting standards before structures but is really putting structure first by the backdoor.
"We need genuine trust and genuine partnership or standards will continue to decline."
But it was not all bad news for the Government. "The tone set so far by education minister Estelle Morris and Professor Michael Barber has been positive and quite reassuring," said one head. "Fair national funding will be the key issue for a happy transfer to new arrangements."
The TES surveyed the country's 1,188 GM schools by post - 755 schools replied, a 64 per cent response rate.
557 74% said they wanted to become foundation schools
8 1% wanted to become community schools
97 13% wanted to become aided
93 12% did not know or answer
357 47% expected recriminations from the local authority
321 41% did not
65 9% did not know
12 2% did not answer
461 61% said they would lose staff
1,164 jobs would be lost in these schools
The top three reasons for going GM
* Bad LEA
The top three achievements
* Value for money services