Ofqual is planning to rate exam boards on the "value for money" they offer schools and assess whether the prices they charge in the pound;300 million GCSE and A-level market are "acceptable".
The regulator will also scrutinise boards on measures including the number of mistakes on question papers, security breaches and quality of marking, it has revealed.
Regular reports on exam board performance will be published from this academic year, according to Ofqual's latest corporate plan. Concerns have mounted as exam fees consume ever larger proportions of secondary school budgets, and headteachers have welcomed the prospect of greater scrutiny of the boards.
Last year, Ofqual estimated that schools and colleges in England were spending pound;304 million annually on entry fees for GCSEs and A-levels. It has been suggested that this sum could shrink as reformed exams with a linear rather than a modular structure are introduced and the number of resits is reduced.
However, headteachers are concerned that any savings will be cancelled out by the huge costs of reforming A-levels and GCSEs, which exam boards are having to shoulder.
Richard Sheriff, headteacher of Harrogate Grammar School in North Yorkshire, has spent pound;217,000 in exam fees this year, up from pound;190,000 the previous year. He said he was not getting value for money.
"Exam fees are a very big issue for us," he said. "We are very, very concerned about the escalating cost of exams. It is a very significant part of our budget and yet it is one we struggle to have controls over because obviously we are not going to penalise children by not entering them in exams.
"It is a very good idea to look at this. The only fear I would have is if it drives costs down without having an absolute focus on costs and integrity. Then it would be a huge mistake."
Brian Lightman, general secretary of the Association of School and College Leaders (ASCL), said he feared that development costs incurred by the new qualifications would be passed on to schools.
"I would say that the biggest driver in the increased cost of examinations at the moment is the vast volume of reform," he said. "The quantity of changes that are being implemented at the moment are bound to cost money which the awarding bodies will need to recoup."
Mr Lightman added that there was "no evidence" that the move to linear exams would cut costs. "In many cases, young people will be doing more exams because of the large number of final exams in some of the courses such as A-level."
Figures released in 2011 showed that the total amount paid out by secondaries in England in exam fees had almost doubled in seven years. According to Malcolm Trobe, ASCL deputy general secretary, many schools are now spending more on exam fees than "basic learning resources" and "the current examination bill for a 1,200-pupil 11-18 secondary school would probably be in excess of pound;100,000".
But earlier this year Glenys Stacey, Ofqual chief regulator, said that GCSE exam fees represented "remarkably good value for money" because at "less than pound;30, with marking included" they cost less per pupil than the price of "a good meal for two".
Ofqual's corporate plan for 2014-17 (see bit.lyOfqualPlan) says the regulator will seek to develop "efficiency benchmarks" to help evaluate whether boards provide value for money and "the acceptable price of qualifications".
"We will be monitoring the exam boards regarding the future prices for reformed GCSEs and A-levels and the information they provide for schools and colleges," an Ofqual spokesman added. "We will also be looking into the likely impact on costs to awarding organisations of the changes being made regarding vocational qualifications."
Simon Lebus, chief executive of Cambridge Assessment, which runs the OCR board, urged Ofqual to consult on how boards would be judged. "There are obviously dangers in conflating hard measures - such as the number of question paper errors or the number of enquiries about results - with judgemental measures like value for money," he said.
Is the price right?
Latest Ofqual figures on annual income of GCSE and A-level exam boards, including costs of exam entries, textbooks and other services
Pearson Education (formerly Edexcel) pound;510.6m