The head of the funding council has admitted he is baffled by the £600 million of unspecified cuts to the higher education and science and research budgets, and said he had "spent a whole day" trying to figure out what it means.
The Government said in December's pre-Budget report that the savings, to be made in 2011-13, would come from "a combination of changes to student support within existing arrangements; efficiency savings and prioritisation across universities, science and research; some switching of modes of study in higher education; and reductions in budgets that do not support student participation".
Sir Alan Langlands, chief executive of the Higher Education Funding Council for England, told the Lord Dearing memorial conference in Nottingham: "I spent a whole day trying to figure out what it means and I still don't know. We're not going to know for some time to come."
He added: "At some point we're going to have to discuss the £600 million. I for one am not willing to concede that Hefce funding suffers disproportionate pain."
Paul Marshall, chief executive of the 1994 Group of smaller research-intensive universities, has previously said that most in the sector fear that the £600 million will come from Hefce's budget.
With cuts for 2010-11 taken into account, this would leave the funding council having to absorb a £915 million cut between 2010 and 2013 - a 12.5 per cent reduction in its budget over three years.
Sir Alan said it was vital that the standing of England's higher education system be maintained through the tough times ahead.
"We must establish without doubt, in the eyes of the public and our political masters present and future, that higher education is a fundamental part of the solution to economic challenges, not part of the problem," he said.
But he added that the academy's case for investment would have to compete with the claims of schools, health and policing, as well as the "elephant in the room" - the UK's £178 billion budget deficit.
Hefce had "worked hard" to minimise the effect of cuts on higher education, Sir Alan said.
But he added that "some universities will only manage this difficult period by reducing costs and probably jobs, and, I think, developing new ways of working".
This included "more focused and distinctive missions", as well as collaborations with other universities, he said.