Stormont must cough up £85m annually to fund higher education or student fees will have to be raised, minister Stephen Farry has warned.
In an interview published in today's Belfast Telegraph, Mr Farry added stark choices had to be made.
Universities in Northern Ireland receive around £2,000 less per student than their counterparts across the water.
England makes up the difference by charging higher tuition fees, while the Scottish Executive provide funding so that Scottish students do not pay fees to study at local universities.
But Mr Farry said that here in Northern Ireland, universities were getting hammered on both sides.
"They are not able to charge higher fees and they are also seeing their funding from the Northern Ireland Executive being cut back," he added. "One way or another, something has to give."
The minister told how, in an ideal world, he would not want to see students paying any tuition fees but said that people have to be realistic.
"We need something financially tenable over the medium to long-term so we don't have, from one Executive to another, uncertainty over what is going to be in store for higher education," Mr Farry said.
"If we want to go down the route where we are maintaining fees at the level of inflation, then that has to mean that we invest more from our own block grant in higher education.
"That means choices having to made at the expense of other areas or seeing other reforms or seeing other types of revenue-raising being explored to balance our books. There is a very stark choice out there that has to be made."
Mr Farry also claimed that the Northern Ireland Executive would need to provide an extra £85m in funding for higher education each year to get to where universities should be.
"We presently have the situation where, on top of the £16m cut that has been passed on this year to higher education, we had a pre-existing structural deficit that is close to £40m," he said. "So to fix higher education in Northern Ireland will cost in the region of £56m.
"If people want to see an expansion at Magee on top of that, you are talking about an annual recurring cost of around £30m. For an expanded higher education sector in Northern Ireland that other political parties would like to see, we are talking about a commitment of £85m from the Executive per year. That would be for higher education alone."
Mr Farry is set to be the last Employment and Learning Minister, with the department set to become part of a new Department of the Economy after next year's Assembly elections.
He said he felt "incredibly privileged" to have served as a minister for the past four-and-a-half years, and added that he hoped to achieve much more in his final few months in the position.
The minister also revealed that he counted developing new systems for apprenticeships and youth training as his greatest accomplishment in the job.
"It is about applying the traditional model of apprenticeships - often associated with low skills - with the whole full spectrum of skill levels and applying it also to any occupation that demands practical training," he said.
"We have our first higher apprenticeships in place. They are still in pilot form, but we have 500 of those opportunities from this autumn on, and we hope to build on that over the coming years."
But Mr Farry also told how he had been frustrated by the massive budget cuts his department has faced, and said they had seriously impacted upon his ability to implement policy changes. And he added that people would suffer if the Executive failed to invest in youth.
"As we look ahead to future budgets, we need to have a better balance between how we invest in the needs of today in terms of public services and also plan effectively for the future," he said.
"We are not going to see people's wellbeing immediately suffer in terms of the cuts passed on to my department, but most people recognise that what is happening with the cuts to our colleges and universities is very self-destructive."
Mr Farry added that, despite his frustrations, he wanted to see the future of education secured before leaving office.
"It is probably the biggest challenge the sector has been faced with for a generation," he said. "If I walked away from this, I would be very irresponsible in terms of my duties as a minister."
Full interview, pages 20-21