Universities have warned they will still need billions of pounds from taxpayers even if top-up fees of £3,000 are charged from 2006.
Students have fought the government's plans
Vice-chancellors in England and Northern Ireland have asked for £8.7bn in the government's spending review covering the three years to 2008.
Their organisation, Universities UK, said higher fees would have had only a "minimal" impact by then.
It said building repairs and wage increases were adding to costs.
Scottish and Welsh universities have yet to make their bids.
The last UK-wide bid, three years ago, was for £9.9bn.
This prompted the government to bring in its "variable fees" policy.
If this passes, universities in England would be able to charge as much as £3,000 a year for courses. The current flat rate is £1,125.
Universities UK said the £8.7bn for 2005-8 was still needed because, despite increased investment in the last couple of years, academics were still under-paid.
Its members also needed to take on an extra 30,000 students a year, under government plans to expand higher education.
Its president, Prof Ivor Crewe, blamed "real cuts in funding over a 20-year period on a sector you want to expand" for the demand.
Universities UK said the England and Northern Ireland bid did not take into account income from top-up fees, which would total £1.4bn a year from 2009 if all courses cost the maximum £3,000.
'Decades of under-funding'
The Higher Education Bill is currently undergoing detailed scrutiny by MPs.
It got through its first Commons vote last month by just five votes.
Universities UK's chief executive, Diana Warwick, said it had never claimed the government's proposals for a graduate contribution scheme would meet the funding gap.
"No single source of income will do that."
Within the England and Northern Ireland bid, £3.75bn was needed for making up a shortfall in investment in buildings, laboratories, lecture theatres and other infrastructure.
Universities needed an income surplus of between 3% and 4% a year "for reinvestment and to fund future developments".
But the sector's shortfall was set to increase from £290m last year to £357m in 2006-7, which could see up to a third of universities running deficits within three years.
The Higher Education Minister, Alan Johnson, said: "The estimated funding gap is a global figure and is the culmination of decades of under-funding dating back to the 1980s."
But the Shadow Education Secretary, Tim Yeo, said: "The universities say they need all these extra billions of pounds, yet the government has a history of clawing back money with the introduction of extra fees.
"It is time the government made clear what its plans are."
The Conservatives are currently reviewing their policy on university funding.