The investigation by the Qualifications and Curriculum Authority could lead to a cap on future price rises and follows complaints from schools and colleges that they spend an average of pound;400,000 a year on exam entries.
Prices have climbed above inflation for every exam since 2003 despite the Government giving exam boards pound;32 million to "modernise" their systems since 2004. Inflation over the period was 8 per cent.
A TES analysis looked at the cost of exams offered by England's three main boards - Edexcel, AQA and OCR. It reveals that the most expensive course is a 12-module vocational A-level offered by the OCR board and taken by 5,406 pupils, which costs pound;190.20.
It can cost up to pound;164.80 to enter a student for an OCR national, another work-related exam taken by a few thousand students.
The analysis looked at the cost of exams since 2003 and shows that the biggest price hikes have been for vocational courses and diplomas.
Edexcel's BTEC diploma in foundation studies cost pound;85 per pupil in 2003. This year, the price is pound;146, a 72 per cent increase. Edexcel's general national vocational qualifications now cost pound;99 per student, a 45 per cent increase. The board has also amassed at least pound;5 million from its successful new diploma in digital applications courses (DiDA), introduced last year. Edexcel says it has 120,000 registrations for the course, which is widely seen as the successor of the hugely popular GNVQ in information communications technology.
Across mainstream GCSEs and A-levels, price rises have ranged from 14 to 26 per cent (see box). AQA's fees increased most, while Edexcel is the costliest board.
Don Goff, exams officer at John Kelly boys' in Brent, north London, which spends pound;30-pound;40,000 on exam fees, said: "There is a great pressure on schools to get pupils qualifications, so we are almost compelled to pay these prices. If they go up above inflation, it means something else in the budget has to be cut."
The QCA will report on GCSE and A-level prices in the autumn.
Investigations into other courses could follow. If it does act, it will be the first fee cap since its inception in 1997.
Isabel Nisbet, QCA director of regulation, said: "We want to make sure the prices charged are good value for money. I am going to look hard at price increases. But I am keeping an open mind about what would be reasonable."
The boards say they have invested millions and introduced new marking technology in recent years, a point Ms Nisbet backed.
Julian Gravatt, the Association of Colleges' director of funding and development, said the fees were the price that education paid for its "addiction to external assessment".
Recent accounts for AQA show the board had a pound;4m surplus on income of pound;151m in 2003-4. At OCR, the surplus for the same year was pound;2m from pound;84m income. Edexcel figures are not available.
In February, The TES revealed that schools are now spending pound;120m more on exam fees than they are on books.
An Edexcel spokeswoman said: "Edexcel welcomes the widening of Isabel Nisbet's role to include pricing and we are confident she will agree that our qualifications are extremely good value for money."
She said the board had spent at least pound;1.5m, over several years, developing DiDA.
An OCR spokesman said that, as a not-for-profit body, the board strove to offer the best possible value, investing any surplus made from fees in improving qualifications.
An AQA spokesman said the board had engaged in "an enormous amount of work"
developing courses and that unlike other boards, it does not charge extra for less popular GCSEs and A-levels.