Tim Boyes, head of Queensbridge school, a comprehensive in Moseley, Birmingham, blames the boom in vocational qualifications for the rise in the amount secondary schools spend on exam fees.
"The rush into GNVQs has created a black hole in school budgets," he said.
Queensbridge held out against what Mr Boyes calls "the big GNVQ fiddle" - popular vocational courses count for four GCSEs in the league tables - but a small number of pupils are now taking the course in ICT.
"I was horrified when I saw the breakdown of what this is costing us. GCSEs can cost around pound;17, while a GNVQ costs pound;100. I honestly do not know how the exam boards justify this."
Mr Boyes said that Btecs were also a big drain on resources. Exam fees for the two small groups of students at Queensbridge doing the Btec in PE and sport were around pound;100 each.
At the same time, Mr Boyes said the cost of conventional exams had gone up, and the boards imposed heavy penalties on heads of departments wanting to make last-minute changes.
He said spending on books was not a priority for schools wanting to raise standards, arguing that appointing good teachers and support staff was more important.
John Hall, head of Hagley Park high in Rugeley, Staffordshire, said that not only was the cost of individual exams going up, but students were taking more exams, and more retakes in the sixth form.
"My biggest concern is that this is an agenda driven by league tables," he said. "Why have we got this tremendous drive for exams? So the Government can show it is improving standards.
"Our students can potentially take 13 and a half GCSEs. Do they really need all that?"
Next year he hopes to reduce the number of courses taken by each student and their exam workload.
"We did GNVQs for the first time last year," he said. "We did not want to, but there is enormous pressure on schools to improve their GCSE results."
Mr Hall said the percentage of students gaining five or more A*-C grades in GCSEs at the school rose by 15 per cent to 48 per cent last year, mainly because of GNVQs.