The Labour leader has warned higher than expected tuition fees could mean cutting tens of thousands of university places in England.
Ed Miliband demanded answers from Prime Minister David Cameron - as latest figures show three quarters of universities plan maximum £9,000 fees.
Ministers had budgeted for average fees of £7,500 - saying universities charging £9,000 would be "exceptional".
A government spokesman said it did not plan to cut student numbers.
A Department for Business, Innovation and Skills spokesman said: "Even if the average tuition loan goes above £7,500 this would be affordable within the overall higher education funding budget and there is no evidence at this stage that there is any funding gap.
"Because of extensive fee waivers and bursaries which universities plan to make available we will not have a precise figures until late next year, when students have enrolled and received their loans."
But Sally Hunt, leader of the UCU lecturers' union, said: "This policy has become a runaway horse and, without strong intervention soon, could have disastrous effects for our future higher education system."
A higher level of tuition fee, from its current capped level of £3,290 per year, will mean higher up-front loans to students - and there have been warnings of a "black hole" in the higher education budget.
The warning comes on the deadline day for universities to submit their plans to the Office for Fair Access for 2012, the first year of the new fees regime.
Almost 70 higher education institutions - more than half - have declared their plans for tuition fees - and more than three quarters of these want to charge £9,000 for some or all of their courses.
The full picture of tuition fees will not be known publicly until July, when the Office for Fair Access confirms the fees that it has approved for each university.
But Mr Miliband predicted the cost of loans could be up to £500m more annually than expected.
Based on House of Commons Library figures this would put 36,000 university places at risk, he said.
He told reporters in London: "David Cameron said £9,000 fees would only be charged in exceptional circumstances.
"Today we know that £9,000 is not going to be the exception. Every single one of the leading Russell Group university is to charge £9,000. David Cameron looks set to break his pledge.
"He claimed that the new package, higher fees and and a much reduced teaching grant, would save the taxpayer £2.9bn.
"Now with most fees being between £8,000 and £9,000 the government will have to pay out even more money in loans."
He added: "Whatever the exact number there will be a shortfall in government figures and a shortfall in HE [higher education] funding is a double jeopardy for young people."
And he challenged the prime minister to say whether he planned to cut student numbers or university budgets still further.
Ministers have accepted privately that a significant number of students will be paying higher fees.
But they reject any suggestion of a financial crisis, arguing fee waivers and cheaper degree courses in further education colleges and offered by private providers will lower the average cost.
They also claim that because the Treasury will ultimately recoup two-thirds of the amount loaned to students the extra expenditure is not as serious as it may seem.
Universities minister David Willetts played down the likelihood of a black hole in university finances.
He said because of the fee waivers many students would pay less than the published price, and would therefore borrow less.
Aaron Porter, the outgoing president of the National Union of Students, accused the government of causing "costly chaos" with its university reforms.
A White Paper setting out how higher education will be reformed in England is expected in the summer.