They fear the shake-up of the post-16 sector by Sir Ron Dearing will push the cost even higher, with pressure for more students to gain more qualifications.
And they claim that some schools are now not entering pupils for exams that they know they will fail.
Carole Whitty, from the National Association of Head Teachers, said: "Heads are being a little bit more sensible in terms of looking at where students are definitely not pass material, whereas in the past, before local management of schools, we tended to put everyone in just to give them a chance."
Headteachers claim neither Government nor local authorities are prepared to give them extra money to cover the rising costs of exams.
Mrs Whitty, head of Carisbrooke High in Newport on the Isle of Wight, disclosed that the curriculum budget at her school was now just Pounds 3,000 more than the amount it spent on exam fees. "The majority of our students are doing nine or 10 GCSEs," said Mrs Whitty, a national executive member of the NAHT.
A pilot project offering general national vocational qualification part one to 30 students from September will cost the school Pounds 60 per pupil - and many will be entered for GCSEs at Pounds 15 a time.
Mrs Whitty said that modular A-levels were also costly.
"We are spending more than Pounds 60,000 on exam fees this year and Pounds 63,000 on the curriculum. We are almost putting as much money into exams as into the whole curriculum development."
Another school on the island, with 1,400 pupils aged 13 to 18, is looking at an Pounds 80,000 bill.
The NAHT's secondary committee meets today to discuss the rise in costs.
Mrs Whitty said: "I have no idea how schools are going to cope. We are a healthy school financially and able to move money around, but this is going to be a serious problem for schools unless local authorities find the cash to back schools."
Arthur de Caux, senior assistant secretary education with the NAHT, said recommendations from the Dearing review for new applied AS levels, a national diploma and national certificate would increase costs dramatically.
"The pressure of performance tables and the almost mandatory entry into national curriculum subjects means that costs have already gone up significantly."
He said Government had to fund the increases and said: "Schools are never funded to deal with these things. It is just classic.
"People will say Sir Ron Dearing's diploma is voluntary, and we can't put money into something that is voluntary. Nevertheless, everyone says we ought to be doing it and schools will end up doing it without any extra money. Government has got to supply the money in the first place."