The fate of more than 600 places for bright children from low-income families in 118 prep schools joining the scheme this year will be uncertain under a Labour government, even though the party has agreed to honour places already offered if it wins power, the schools said.
Some said they were now unlikely to wait for an end to the confusion and would offer the places to paying families instead.
The difficulty rests on the fact that prep schools new to the assisted places scheme have been forbidden to make any firm offers of places until they receive signed "participation agreements" from the Department for Education and Employment.
The deadline for providing the department with information for the agreements fell yesterday, by which time all processing of the scheme had been suspended for the duration of the election campaign.
Schools will now have to wait until after 1 May to make formal offers of places. They will also have to wait to see whether, if Labour wins, the new government will honour the offers.
Moves to extend the assisted places scheme were included in the Education Bill, which was rushed through Parliament last week to beat the election deadline.
In a series of deals between the parties over clauses in the Bill, Labour said children who had accepted offers by 1 May would be allowed to take up their assisted places if it took power, though it remains committed to phasing out the scheme and using the money saved to cut class sizes.
Private prep schools which have been allocated assisted places yesterday confirmed they had been told not to fill them without the formal agreement.
Andrew Corbett, headmaster of Kings College School, Cambridge, predicted a new Labour government might argue that the school could not offer its allocated five places.
He said: "Having publicly announced it was awarding these places, it now looks as if the DFEE are going to turn round and say they are not. Parents have had their hopes built up, and we have to turn round and say no, unfortunately we can't offer them."
George Marsh, headmaster of Dulwich College Preparatory School in south London, said May was likely to be too late to fill places for many schools, forcing them to give up their allocated assisted places.
Labour yesterday confirmed "any places allocated to a specific individual children" by election day would be honoured.
A party spokesman said the situation would be reviewed in the light of the freeze on agreements, but blamed government incompetence in pushing through the bill for creating the problem.
The spokesman added: "They did not have the necessary commitment behind what they apparently regard as flagship proposals."
A spokeswoman for the education department said that all processing of participation agreements had been stopped until after the election in line with guidelines on dealing with long-term commitments during an election period.