Along with cuts to higher education funding and allowing universities to set their own fees, the Coalition is pushing to increase the interest rate for HELP loans in 2016 by changing it from an inflation rate equivalent to one that ''reflects the cost of government borrowing''.

When asked on the ABC's Insiders program if students who are enrolling today or next year would be repaying their debts at a higher rate, Mr Pyne replied: ''Anybody who was enrolled before May 14, nothing will change in terms of their arrangements.''

The government's Study Assist website clearly states that the new indexation arrangements will ''apply to all HELP debts (including those incurred by former students, continuing students and new students) continuing and new students beginning with the indexation of debts on 1 June, 2016''.

There have also been wobbles from Prime Minister Tony Abbott and Treasurer Joe Hockey while explaining budget measures.

Labor said Mr Pyne's response was a sign the government did not know what was in its own budget. Labor's higher education spokesman, Kim Carr, said Mr Pyne was either ''very confused'' or he was ''seeking to mislead''.

Mr Pyne's office said he was referring to ''any changes in fees'' not impacting upon existing students, rather than the repayment rates for loans.

The confusion came as one of the country's most senior academics warned that the government's proposed changes to higher education would result in a ''social experiment without precedent in Australia'' as students from poorer backgrounds dealt with university fees that are set to soar by up to 60 per cent.

Melbourne University vice-chancellor Glyn Davis said there was no way of knowing in advance how students would respond to the pending fee increases. While acknowledging Britain did not report a long-term fall in such enrolments when it deregulated fees, Professor Davis said it would be ''very distressing'' if students from poor backgrounds were no longer as willing to sign up to university degrees.

Professor Davis also suggested that the reforms were unlikely to pass the Parliament in their current state, leaving the higher education sector in a state of uncertainty.

''I don't think any of us know what the real package will end up looking like, including possibly the minister,'' he said.

Professor Davis said even though he had advocated for fee deregulation, it was not a call for cuts to public funding. ''It's hard in those circumstances to see how we're going to proceed without at least making up the money we've just lost [through increasing course fees].''

On Sunday, Mr Pyne played down the likelihood of soaring fees as a result of the budget.

''If universities think they can get away with charging exorbitant fees, you will find they face intense competition,'' he said.