Secondary schools applying for specialist status have been assured they will not be thwarted by this year's budget shortfalls.
Some schools which have had to set deficit budgets, through no fault of their own, feared their bids would be turned down.
The Liberal Democrats, who highlighted the problem, said the education secretary should make it clear the schools would not lose out.
Officials in the education department have done so - stressing that applications are assessed on their future plans not past performance.
There are currently 1,454 specialist schools in England, 46% of the total. The latest 245 took up their status this term.
Schools bidding for specialist status have to raise £50,000 in sponsorship and put together a four-year development plan for raising standards in all subjects.
Successful applicants receive a grant of £100,000 plus an extra £123 per pupil per year.
One school that is preparing an application is the Priory School in Orpington, Kent, a 1,500-student mixed comprehensive in the Bromley education authority.
It hopes to gain dual status as a business and sports specialist.
The associate head, Tim Pike, said it was between £200,000 and £300,000 short this year on the kind of funding it used to have.
It had formally asked Bromley for permission to set a deficit budget, which had been agreed verbally.
The school had taken advantage of the freedom granted to schools by the Education Secretary, Charles Clarke, to raid their capital budgets for ongoing costs this year, which provided about £70,000.
Cutting the teaching week to the recommended minimum of 24 hours, from its current 25, would save the equivalent of about three teachers over a year - about £80,000.
"But it takes time to work through, so it won't help us this year," he said.
Other savings could be made "but we are not prepared to be silly about it".
"Under the rules of specialist school status you cannot be in a deficit budget situation at the time you make the application.
"So we could find ourselves in a Catch-22 where obtaining the status would give us the extra money, at least in part, but we may have no chance of success."
The Liberal Democrats' education spokesman, Phil Willis, said: "This year hundreds of aspiring schools have been forced to set deficit budgets as a result of ministerial incompetence and may lose out on specialist status as a result.
"It is crucial that the secretary of state makes it clear that schools will not lose their bid for specialist school status and should continue with their applications."
But the Department for Education and Skills said the fears were groundless.
"Schools facing a budget deficit this year will in no way be disadvantaged in their bid for specialist status," a spokesperson said.
What the department took into account was a school's vision for its future and that of its local area.