Research councils will have to make millions of pounds in cutbacks after the imposition of new government accounting techniques.
The amended rules rigidly separate capital and resource budgets that previously could be used to balance each other.
Research council representatives are negotiating with the Office of Science and Technology to try to get a dispensation from the Treasury to transfer unspent funds locked in demarcated accounts.
The Natural Environment Research Council said it would have to find £14 million-worth of savings over the next two years.
The impact of these cuts would be felt mainly in centres such as the British Antarctic Survey, the British Geological Survey and the Proudman Oceanographic Laboratory. Some initiatives will be delayed, departing staff not replaced and the refitting of ships put back.
Further cuts, including postponing next October's responsive mode grants, may be necessary if some funds were not recovered.
David Bloomer, Nerc's finance director, said the council had a £5 million underspend on capital and a £4 million overspend on resources.
It had also handed the OST £5 million of unspent cash at the end of the financial year and had budgeted to get it back only to learn this would not happen.
In addition, Nerc had overcommitted £10 million to two years of research spending in the expectation that the uptake of funds would leave some headroom.
Mr Bloomer said that under the old rules, it would have been able to balance its budget and manage its way through the grants overcommitment.
He said Nerc had been informed about the rule change only in January, and while the OST was trying to recover £5 million from the Treasury, he was resigned to losing at least £4 million.
The Medical Research Council would not reveal how much of its money had been caught up in the administrative system. But a spokeswoman admitted that there were discussions with the OST concerning a "small fraction" of the MRC's £372 million budget.
David Schildt, director of corporate development at the Central Laboratory of the Research Councils, said a knock-on effect was expected. "Should such (budget) constraints be realised, we might expect that they would have some impact on programmes the research councils fund in the CLRC," he said The £12 million of savings being made by the Particle Physics and Astronomy Research Council have been blamed on a combination of government funding not keeping pace with inflation and the cost of international projects.
An OST spokeswoman admitted the accounting changes had forced each research council to reassess its financial commitments in the short term, affecting a "very small proportion" of their budgets.
Peter Cotgreave, director of the pressure group Save British Science, complained that scientists would bear the brunt of cutbacks inspired by "pencil pushers".