Academics and MPs reacted with anger this week to news that research councils had accidentally underspent by millions of pounds, while top-rated research proposals are being turned away.
The Medical Research Council told The Times Higher this week that it had unexpectedly underspent by £52 million from its 2004-05 budget of about £500 million.
The other councils were unable to provide comparable total figures on their underspends.
But in their public accounts, the Particle Physics and Astronomy Research Council reported an underspend of £15 million, the Engineering and Physical Sciences Research Council reported an underspend of £6 million, and the Natural Environment Research Council reported an underspend of £5 million.
Council sources said internal figures agreed with the Office of Science and Technology showed that actual deficits were several times larger than these figures.
The councils said this week that the situation would not have affected researchers' chances of winning funds this year.
But at a time when many councils report record numbers of applications and very low success rates, the news will be a big blow to researchers'
morale.
Funding for new grants has doubled in the past two years at the MRC, but the proportion of successful proposals has dropped to 15 per cent, and the council is still unable to fund all of the highest-rated internationally excellent proposals.
One senior medical researcher said: "This is a tenth of the MRC's budget we are talking about. The community will be livid. There were financial problems at the MRC three years ago, and that caused all sorts of problems.
It was really miserable. It is clear that the MRC's accounting is appalling."
He added: "Funding is enormously tight, and I know a lot of people who feel they have good ideas and aren't getting a fair crack of the whip."
Evan Harris, Liberal Democrat MP and member of the House of Commons Science and Technology Select Committee, which criticised the MRC's accounting in 2003, said: "This is something that the select committee will want to look at across all the councils."
Peter Cotgreave, director of the Campaign for Science and Engineering in the UK, said: "Of course there will be reasons for this, but on the ground that is no comfort for scientists with great ideas who have been told that Britain is the best place to do research but who cannot get funding. If I were the Chancellor, I would be very angry."
One university science dean said: "I don't think many people know about this; so it will cause quite a stir."
But Colin Blakemore, MRC chief executive, said: "There is a crucial difference between money committed during the year and money spent. Most of the annual spend comes from commitments made in previous years.
"The obvious concern of researchers is that unsuccessful applications should have been funded, but this is absolutely wrong. We committed almost all the money to new grants that we planned to."
He said that half the underspend was due to delays in starting previously awarded grants. And £9 million of the leftover sum was unexpectedly returned by universities unspent at the end of grants. The council also had staffing problems in its financial department.
Professor Blakemore said the MRC had budgeted more conservatively than other councils because it had overspent in the past.
However, he added: "You might think that we could have poured that £52 million into new grants as soon as it became clear that we were going to underspend. But that would not have affected the underspend because the money would not have been spent until later years. And the burst of extra grants would have produced a repeat of 2000-03, plunging us into a cashflow hole with decreasing money for future grants."
Stuart Ward, chair of the operations management group at Research Councils UK , the councils' strategy group, said the leftover money was an inevitable result of "dynamic" financial management. He said it would in effect remain in the hands of the Office of Science and Technology and would not be snatched back by the Government.
He said: "We try to avoid big fluctuations from year to year in the level of new grant commitments. Each of the councils has a delivery plan and there is a planned commitment for three years."