In Lincolnshire, the education authority is picking up a 1 per cent charge for distributing school achievement awards, after headteachers were initially told they would have to make the same deduction from their individual awards.
Department for Education and Employment guidance on administering the awards says payroll suppliers may make small administrative charges. A department spokeswoman said the level of charge was down to the school and payroll supplier, and that other areas could be affected.
Around 7,000 English schools are getting the awards, averaging around pound;5,000 for primaries and pound;25,000 for secondaries The money has to be distributed as staff bonuses in recognition of improvements in pupil performance.
However, shortly after announcing the winners, ministers admitted calculating errors had led to around 300 schools missing out on awards - and another 300 schools getting money they had not earned.
They were allowed to keep the cash but missed out on certificates and official recognition.
Richard Hall, head of Branston junior school, Lincoln, said the administrative charge was like "patting you on the back with one hand, and taking away with the other".
"The staff were very appreciative of the award, and hadn't expected it. But it's a curious state of affairs to be rewarded and then to have to pay for the privilege," he said.