Severe cuts in capital funding for the seven bodies which distribute taxpayers' money to scientists will create "particularly significant challenges", their representative council said today.
At the same time, the research councils breathed a collective sigh of relief at not having suffered more.
Science emerged from October's Comprehensive Spending Review (CSR) with its £4.6 billion budget ring-fenced for the next four years.
Taking inflation into account, this amounts to a cut of about 10% by 2014-15 which, it was hoped, could be offset by "efficiency savings".
However, the CSR settlement did not cover capital spending on buildings, equipment and maintenance, and today, as the Government announced individual budget allocations for the research councils, it was revealed that science infrastructure funding will be slashed by around 40%.
Professor Alan Thorpe, chair of Research Councils UK, which represents the funding bodies, said: "The cut to the capital budgets of the research councils will present particularly significant challenges going forward but we have a good foundation, and excellence with impact will remain at the core of what we do."
He said it was encouraging the research council allocations had "fared so well" given the tough economic climate.
"This allocation as part of the 2010 spending review confirms the value that Government has placed on research investment for the UK," Prof Thorpe added.
Imran Khan, director of the Campaign for Science and Engineering, said the budget announcements confirmed that British science and engineering faced four "very tricky years".
Although capital spending on research was being hit less hard than expected, the cuts still amounted to a "dramatic reduction" in investment in equipment and facilities.
This would produce a "big dent in Britain's scientific credentials".
Mr Khan said: "What's especially worrying is that a lot of this capital spending is actually maintenance and other long-term commitments, which can't simply be stopped. The money will have to come from other sources, including research grants, instead.
"There are going to be a lot of very difficult decisions which have to be made over the coming years."
Bob Ward, policy and communications director at the Grantham Research Institute on Climate Change and the Environment at the London School of Economics, said applying the latest inflation forecasts showed that science capital funding could be cut by almost half in real terms.
"Today's announcement confirms that the Government is planning to slash capital expenditure for research," said Mr Ward. "It looks like we could be returning to the dark days of the 1980s and early 1990s when researchers were forced to work in laboratories and facilities that were starved of investment.
"World-class researchers need world-class facilities and infrastructure if they are to provide the advances in knowledge and innovation that drive our economy."
Factoring in the reduced capital expenditure, publicly funded research as a whole will lose around 14% in real terms rather than the 10% projected by the CSR, he said.
While other research councils will see their resource allocations cut by around 3% by 2014-15, the Medical Research Council's share of the pot is being increased by around 5%.
Universities and Science Minister David Willetts said: "Our world-class science and research base is a key national asset, critical to promoting economic growth and to improving all our lives.
"This is a strong settlement which demonstrates the importance the coalition Government places on science and research."