Expectations of a spectacular spending review settlement for science were dashed last week as research councils discovered how little new money would be available for science projects.
The Government is not expected to announce the research councils' budget allocations for the three years from 2005-06 for another week.
But senior research council figures privately expressed disappointment and anxiety this week, after a preview of the figures.
One source, who asked to remain anonymous, said: "The headline figure looks like a substantial increase but the amount of money for new science is actually very small. Some of the councils may be in real trouble."
Hopes had been running high in the science community after Chancellor Gordon Brown's ten-year investment framework for science, published in July. This promised major increases for science funding, with the research councils allocating some £3.3 billion to universities and research institutes by 2007-08.
The bulk of this extra cash has already been earmarked for the battle to make universities more sustainable - including a rise in PhD stipends and a commitment by the research councils to pay 80 per cent of the full economic costs of all research projects for the first time.
While the councils are unanimous in their approval of such measures, some admit privately that they will be in a difficult position without more money to fund new science.
According to one source, after all the sustainability costs are factored in, only one research council will end up with a real-terms increase to its budget by 2008.
Research council chief executives are now debating how to dampen the expectations of the science community and avoid a flood of new research applications that cannot be funded.
A second research council figure said: "If we are not careful, people will think there is lots of money and, because of full economic costs, universities will want researchers to bid for more research council grants. The worry is that there will be two or three years during which we will be deluged."
But Julia Goodfellow, chief executive of the Biotechnology and Biological Sciences Research Council, said: "There is pressure on vice-chancellors to run a sustainable institution, so the fact that they will have to find the remaining 20 per cent of full economic costs for research council grants should act as a sort of control.
"Getting research properly funded is an amazing challenge and it is absolutely fantastic for the community. It is ridiculous to have to say that every time someone takes on a grant it is a loss-maker - and in the biosciences we know the costs are going up as we move towards big science."
Robert Key, the Shadow Minister for Science, challenged Lord Sainsbury about the lack of money for new science in a meeting in Westminster on Tuesday.
He warned scientists to look at the small print when the Government announced its allocations.
"Beware of the spin. We need to be careful we don't go overboard and say this is an overwhelming settlement for the research councils," he said.
But Lord Sainsbury replied: "What you need to look at are the total sums of money going in (to science) - they are very impressive. I think it is right that we have full economic costing as a top priority."