More than 1,000 academics could lose their jobs after last week's funding allocations.
The allocations gave about 15 institutions extra money to compensate for large budget cuts. But this cash will be withdrawn after next year, leaving some institutions up to £3 million worse off.
Last week's decision to limit the help given to struggling institutions has been attacked by vice-chancellors and unions alike. Roderick Floud, president of Universities UK and provost of London Guildhall University, said: "The new arrangements impose unsustainable year-on-year changes that work against sensible planning. This will almost certainly mean significant redundancies and course closures."
The Association of University Teachers warned of job cuts in the old university sector, which has been hit by the funding council's failure to fully fund improved research ratings.
Lecturers' union Natfhe said that up to 1,000 academics in new universities could face redundancy as a result of an "outrageous" funding round that would leave 26 institutions facing cuts in real terms.
Cranfield University will lose £3 million after next year under present plans. A spokeswoman for the university said: "We are different to most universities that concentrate on blue-skies research. Our research is of the highest quality but it is just of a different sort. Funding from the council is a smaller proportion of our income, but it is significant."
The London School of Hygiene and Tropical Medicine faces a £1.3 million cut even though it maintained its two grade 5 ratings in last year's research assessment exercise. Dean Andy Haines said: "At this stage, we are looking at our options. I hope that we can avert job losses, but it will depend on detailed financial planing."
The Institute of Cancer Research faces a £1.2 million cut after maintaining its research record. The bulk of its funding is for research.
Other institutions facing cuts include the University of Greenwich; Queen Mary, University of London; the University of Hull; the University of Bradford; St George's Hospital Medical School; Umist, Keele University; and the University of Sussex.
Sally Hunt, assistant general secretary of the AUT, said: "The axe will cut deep across the university sector unless the government takes immediate action to fully fund the latest results of the research assessment exercise. Nearly half of all institutions face real-terms cuts in research funding, which will lead to further redundancies and demoralisation among academic staff."
An AUT spokesman said: "We don't have enough data yet, but we are asking all local associations to be extra vigilant in weeks ahead and to ensure that management don't try any tricks. We will vigorously fight any moves to reduce staff numbers.
"Overall we are deeply concerned by the funding allocation and are demanding an immediate rescue package for research in the budget and then an extension into the spending review in July."
Tom Wilson, head of universities at Natfhe, said that future job cuts would be a particularly cruel blow, given that new universities lost several hundred staff last year through a series of voluntary and compulsory redundancy programmes.
He said that several universities had redundancy plans even before the funding allocations. Oxford Brookes University is already facing the loss of 140 academic staff.
Middlesex University is making six academics compulsorily redundant, Luton University is seeking up to 16 volunteers for redundancy, and the University of East London and Thames Valley University are seeking a "substantial" number of voluntary redundancies.
According to Natfhe, the new universities did particularly badly in last week's grant allocations. Of the new universities, 41 got less than the average increase and only 13 got more. Of the old universities, 24 got above average increases and 17 got less than average increases.
Mr Wilson said: "We were told last year that the cuts were 'tough medicine' that would help institutions to restructure and grow, but we will get more cuts. There is a strong hint that some institutions will be forced into alliances and mergers, and there will be increased pressure for job cuts."
Natfhe pointed out that the 10 per cent premium for teaching students from widening access areas - up from 5 per cent - is still less than half the extra teaching cost. It also said that the money was distributed strangely - for example, the University of Oxford got far more than Thames Valley University.