As Parliament prepares to vote on the future of tuition fees, the chair of council at one of England's elite universities has said publicly that his institution is looking at using income from future fees to meet the "shortfall" in research funding.

Sir Stephen Wall, who leads University College London's council, said that in light of the real-terms cut to the science budget, the institution "obviously" had to consider diverting fee revenue.

His remarks at the recent annual meeting of the Higher Education Funding Council for England, held in London, provoked a stern response from Hefce's director of research, innovation and skills, David Sweeney.

Meanwhile, Aaron Porter, president of the National Union of Students, said it would be "intolerable" if additional fees were used to plug funding "black holes".

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Mr Porter cautioned that universities' books would be "pored over" if the fees hike was voted through, to ensure that money was spent on improving the student experience.

The practice of "siphoning off" money from fee income to fund research is not new - in 2008-09, research spending outstripped research income by more than ?2 billion - but Sir Stephen's comments will be seen as especially ill-timed as student protests and university occupations continue ahead of the fees vote on 9 December.

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Although the science budget will suffer a real-terms cut, it is being ring-fenced in cash terms until 2014-15, a result seen as a major victory for the research lobby.

David Willetts, the universities and science minister, has also expressed his belief that the funding could be completely protected if the research community achieves efficiency savings along the lines suggested in a key report by Sir William Wakeham.

In a question to a panel of senior Hefce managers at the meeting late last month, Sir Stephen said the science settlement "does represent a cut in real terms and so for a big research-intensive university like UCL, that is a real factor".

He added: "One of the things obviously we have to look at is...requiring students through the fee system to fund the shortfall in government support for science and other research."

Mr Sweeney replied: "I would not advise that as a strategy for sustainable research funding.

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"If we are seen to be siphoning off that money to support other activities, we are not, I believe, delivering for our students."

He added: "I think that we have got to be very, very responsible in universities about what we deliver to those students in return for the burden they are taking on."

The Hefce director added that the science budget had got off lightly in the Comprehensive Spending Review and said it was essential that research institutions looked at their cost base to make up any shortfall.

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"We cannot just go forward saying we need the same amount of money," he said.

Responding to Sir Stephen's comments, Mr Porter said: "It would be intolerable if additional tuition fees were robbed from teaching budgets to top up other university funding black holes, which have no direct bearing on the tuition students receive.

"If additional money in tuition fees is sought from students by universities, then the game has changed and every single penny will be scrutinised and pored over to ensure that universities are providing value for money."

He added: "Shoddy practices will no longer be acceptable."

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simon.baker@tsleducation.com