The UK government is looking to make savings of £600m in higher education, and science and research budgets.
The cuts, which will cover the period to 2013, were announced in Wednesday's Pre-Budget Report (PBR).
Campaigners said the move made for "bleak reading" and risked undermining the country's research base.
But a spokesman for the government said it remained committed to its science programme, which has doubled the annual spend to £6bn since Labour took office.
The economies were announced in the documentation that accompanied Chancellor Alistair Darling's PBR, his final such report before the General Election.
The made clear where £5bn of savings should be made by 2012-13, as part of the programme to rein in government expenditure and debt.
It said £600m would come "from higher education and science and research budgets 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."
Dr Beth Taylor, director of communications at the Institute of Physics, said science was not the sector to make savings.
"To see the science base singled out as a 'lower-value or lower-priority programme', whatever the immediate pressures, is short-sighted," she said.
"We need a highly skilled population to restructure our economy or we will be left lagging behind other countries that have taken a very different view of investment priorities."
Her thoughts were echoed by Nick Dusic, the director of the Campaign for Science & Engineering.
"The UK's success in science, and the government's investment in it, will be undermined by £600m savings in the science and higher education budgets. The government cannot afford to undermine the research base if it is going to achieve its goal of a more balanced economy."
Mr Dusic said there needed to be an urgent statement on the status of the government's 10-year science and innovation investment framework. This has sought to raise spending by 2.5% a year in real terms, putting the total science budget on a target for £6.3bn for 2010/11.
A spokesman in the Business, Innovation and Skills (Bis) department told the BBC the government remained committed to its framework but needed also to make efficiencies. A discussion would now take place with stakeholders to identify the best place to make those savings, he added: "We're committed to spend £6bn on science in 2010, which is a doubling since 1997, and nothing today moves us from that framework."