Why 1,001 is an unlucky number
Schools with specialist status are supposed to receive a bonus of pound;129 a year for each pupil.
But the Department for Education and Skills has confirmed the extra cash is only provided for the first 1,000 students on the roll and then for each of those after the 1,201st.
Schools which take on a second specialism get extra money per pupil - but again the 1,001 rule applies.
The curious system has perplexed headteachers and caused Eric Pickles, MP for Brentwood and Ongar, to write to Charles Clarke, Education Secretary, complaining about discrimination against large schools. The Tory MP said six specialist schools in his constituency had together lost out on pound;150,000 a year.
"I do not see any logic behind the decision and believe that specialist schools should receive the additional funding for every single student," he said.
The National Association of Head Teachers was also confused by the funding decision.
David Hart, general secretary, said: "It seems rather strange that large schools should not receive the money for pupils on their roll.
"And it is particularly odd in the context of Labour's five-year strategy for education, which encourages schools to expand."
More than 60 per cent of secondary schools have specialist status, and nearly half of all secondaries have more than 1,000 pupils.
If the Government succeeds in its ambition of making all schools specialist, the funding rule could save it more than pound;37 million a year.
The DfES said it believed the cash provided for specialist schools was sufficient to deliver the aims of the programme and denied that large secondaries were being mistreated.
The Government plans to increase the per-pupil funding given to specialist schools by pound;3 per pupil from September next year meaning an average secondary will receive an extra pound;3000. But the funding anomaly will remain.