The number of students deterred by raised tuition fees is the equivalent to the government shutting the doors of two entire universities, Labour has claimed.
Opening an Opposition Day debate in the Commons, shadow minister Shabana Mahmood said 30,000 fewer students would become undergraduates this month.
But she faced down challenges from the government benches that graduates will face smaller loan repayments in their first graduate jobs under the new scheme.
The coalition increased the cap on tuition fees to £9,000 after taking office but said the repayment scheme would be better for graduates.
Ms Mahmood told the Commons: "We already know there are around 50,000 fewer applicants to higher education for the coming year. One in 20 young people who we would have expected to apply in previous years have not applied this time around.
"As of now, total accepted applicants are down by about 30,000 on last year. That's the equivalent to shutting down two mid-sized universities, say for example Imperial College and the University of Lincoln.
"This is set against a back drop of worsening economic outlook as a result of this government's failed economic policies. The economy is in a double dip recession made in Downing Street and we know there is a strong link between periods of recession and interest in higher education."
Ms Mahmood called on the government to cut tuition fees to a maximum of £6,000.
She said: "We proposed a fully-funded way of doing this paid for by not going ahead with a corporation tax cut for the banks and through some additional payments by the wealthiest graduates."
But universities minister David Willetts said the Conservatives, Labour and Liberal Democrats agreed during their stints in government to fund higher education through making graduates pay through their monthly packets when they find jobs after finishing their courses.
He told MPs: "All three political parties faced with dilemma of how to finance higher education in the future have all essentially concluded the right way forward is a scheme with no payments up front by students but instead with a graduate repayment scheme paid for out of PAYE, incorporating the best features of graduate income tax.
"All three parties when faced with the responsibilities of government have actually reached the same decision."
Mr Willetts said students would receive "well-funded" teaching "while at the same time saving money for the Exchequer because of the fiscal crisis we inherited from the previous government".
He urged MPs against scaremongering, warning attacks on government policy over financing higher education risked confusing would-be students and deterring them from enrolling at universities.
"We should all communicate the message that no student pays up front, they only pay back as graduates," said the Tory minister.