Ministers "significantly" underestimated the number of universities which will charge maximum £9,000 tuition fees, a Government spending watchdog has found.
A Public Accounts Select Committee report says it is unclear whether the fees, treble the current maximum, will deter students from applying to study for degrees.
But it warns of "a substantial funding gap" for English universities which may lead to cuts in higher education or need more taxpayers' cash as the Office for Fair Access bids to encourage more students from poor backgrounds to apply for courses.
The report says: "All the indications are that significantly more institutions will charge significantly higher fees than was anticipated by the Department for Business, Innovation and Skills.
"The Office for Fair Access has yet to agree the measures universities will adopt to widen participation where the proposed fees are above the £6,000 level.
"However, it is likely that a significant funding gap of hundreds of millions of pounds for the taxpayer will occur. Unless further resources are secured by the Department, this could result in further cuts being made to the Higher Education budget."
Committee chairman, Labour MP Margaret Hodge, also said universities' regulatory body, the Higher Education Funding Council for England, would need beefed-up powers once higher tuition fees are introduced and its role in awarding cash to institutions was cut back.
She said: "Unprecedented change is about to take place in the higher education sector as it moves towards a system in which funding for teaching follows the student.
"The Higher Education Funding Council for England will no longer be able to rely upon its funding role to influence the sector and a new system of regulation will be required. At present, more universities intend to charge higher fees than the Department for Business, Education and Skills had expected.
"If the universities' plans to widen participation are approved by the Office for Fair Access, this will leave a substantial funding gap which will either require further cuts in higher education or further resources from the Treasury."