Government plans to scrap GCSEs will lead to schools shouldering the cost of even higher exam fees, the qualifications watchdog and assessment experts have warned.

Education secretary Michael Gove wants just one exam board to offer each qualification as part of his controversial proposals for English Baccalaureate Certificates (EBCs). But exams regulator Ofqual and other experts consulted by an influential committee of MPs have cautioned that this franchising system will result in higher prices or qualifications in smaller subjects disappearing.

The comments were revealed in the Commons Education Select Committee’s critical report on EBCs, published last week, which called on the government to slow the pace of reform.

Schools are already struggling to cope with unprecedented hikes in exam fees. Figures released in 2011 showed that the total amount paid out by secondaries in England had almost doubled in just seven years to an annual #163;302.6 million.

But evidence published by MPs said it could get worse. The report stated that one expert told the committee: “GCSEs were relatively good value for money and ‘I can only envisage prices going up (under franchising)’.”

“One contributor predicted that cross-subsidisation would cease to work and that either the prices for these (less popular) qualifications would increase or the qualifications would disappear,” the report added.

The committee was also told by Glenys Stacey, Ofqual chief regulator, that under a franchising system “pricing would be a dark art, or would be lacking in transparency”.

The report raised a number of other concerns, including lack of coherence, fears about the impact of EBCs on lower-attaining pupils, and damage to other qualifications. It follows criticism of the EBC plans from Ofqual, the CBI, exam boards, prominent Conservative politicians, teaching unions and sporting and arts organisations.

The government is “trying to do too much too quickly”, according to the select committee, which called on ministers to acknowledge the “red light” education experts had shown and to decouple the franchising and EBC proposals.

Insiders have suggested that the franchising system could be jettisoned when the proposals are finalised, despite its position at the heart of the original plan.

Exam boards have already devoted considerable resources to developing EBCs. They are privately warning that if any big changes now lead to that money being wasted, the costs would have to be passed on to schools through higher fees.

Brian Lightman, general secretary of the Association of School and College Leaders, said: “Exam fees already take up a hugely disproportionate amount of school budgets and the last thing we want is any further increases in these costs.”

Questioned by the committee in December, Mr Gove said: “I do not see inherently why pricing should rise as a result of a franchise system.” He added that proposed prices would be a factor in deciding whether a board would win a franchise.

But committee chairman Graham Stuart told him that if the fees were not fixed then he “should recognise that prices will rise”. “If you make the slightest change in requirement as the client then, whoosh, the price will go up immensely,” the Conservative MP added. “There will be no one else you can turn to because we have created a monopoly.”

Mr Gove insisted boards would be obliged to stick to agreements. “Ofqual will have the power to fine or to intervene,” he said.