Business Secretary Vince Cable has unveiled plans for a squeeze on public funding for scientific research.
He urged universities to do "more for less" and said taxpayers should only back research that has a commercial use or was academically outstanding.
Mr Cable said in a speech in London that the government "values" UK science and research and spends £4.3bn a year.
However, Lord Rees, president of the Royal Society, said cutting science funding would be a false economy.
Mr Cable's speech came ahead of next month's Comprehensive Spending Review, which is likely to squeeze resources.
The business secretary urged universities to find ways of earning money from their research, especially from the business sector, in order to make up for limits on public spending.
He told an audience of academics at the University of London: "There is a school of thought which says that government commitment to science and technology is measured by how much money it spends.
"Money is important both for the quantity and quality. But it is an input - not an output - measure. We could do more for less."
Mr Cable added that he supported top-class "blue skies" research, but "there is no justification for taxpayers' money being used to support research which is neither commercially useful nor theoretically outstanding".
The Liberal Democrat minister said that "transforming research into innovation" by linking research institutions to business is crucial.
"It is not a case of ditching scientific research that doesn't offer an immediate economic benefit. But I do think we need to do more to ensure that we reap the benefits of research," he said.
But Royal Society president Lord Rees told the Financial Times: "It is crucial that short-term austerity should not undermine our science and innovation capacity.
"Global competition for the most talented individuals, the most innovative companies and leadership in high-tech sectors is intensifying.
"Cuts would create the impression that UK science is in relative decline and make the UK a less attractive location for mobile talent and investment."
Universities UK also warned that Mr Cable risked sending the wrong message.
Professor Steve Smith, president of the organisation, which represents all UK universities, said funding is already "strongly weighted towards world leading research and internationally excellent research".
He added: "The coalition government is in danger of sending the message that the UK is not a serious player in the field of science and innovation."
And Professor Les Ebdon, chair of Million+, which represents new universities, said: "The UK does not fund mediocre research.
"It funds excellent research which is found in universities throughout the UK. Any proposal to cut the quality related research funding stream would damage the UK's research base and the capacity for future innovation vital to our economy."