Researchers at about ten UK universities may lose out on cash because their institutions failed to prepare in time for the full economic costing model to be introduced next week.
From September 1, academics can apply for a share of an extra £200 million from the research councils to cover the full costs of research, including expenses such as laboratory infrastructure.
Academics will have to include detailed estimations of the time and resources a project requires.
There is no upper limit that can be claimed, although institutions claiming large amounts will be asked for additional justification.
But a number of universities will be eligible for only a flat rate of Pounds 22,000 per researcher and will be unable to claim for laboratory and other estates costs. This is because they missed the deadline to prove that systems are in place to ensure accurate costing of research.
This week, the Higher Education Funding Council for England published quality audits that KPMG consultants had carried out at 166 institutions before February this year.
Overall, KPMG was impressed by institutions' preparations for full economic costing but it concludes: "It is reasonable to expect that further work is still required to successfully implement the requirements of full economic costing."
KPMG still has to report to Hefce on the final number of institutions that will not be ready for September 1.
But Ian Lewis, head of finance at Hefce, said that he expected all research-intensive universities to be prepared, but he believed that about ten institutions would still have work to do.
He said: "There is a small number of institutions where there is still some work to do as they have not not met all the recommendations from the KPMG visits. They will have to apply the default rate.
"There will be another benchmarking exercise next year when we expect they will have met the benchmarking requirements. But the research-intensive universities are ready."
Hefce has said that those charging more than £37,000 per researcher, £10,000 per laboratory or clinical facility, or £6,000 per non-laboratory estates resource may be asked to justify their rates.
Up to now, costs such as laboratory infrastructure or a principal investigator's time were included in the funding council side of the dual-support system.
This was calculated at 46 per cent of these indirect costs, leading to an estimated shortfall of £2 billion in UK science.
Under the new model, most institutions will be able to claim 80 per cent of their indirect research costs for grants starting from April 2006.
The money cannot be used to carry out more research but is there to ensure the research that is carried out in universities is better funded.
Steve Visscher, executive director of the Biotechnology and Biological Sciences Research Council who chairs the cross-research council board for dual support, said that the new system would take a bit of getting used to.
"The first few times, it will take a bit longer. But overall it is good news for the sector," he said.
"The objective is to properly fund the research being conducted so the infrastructure of the UK science base is attractive and robust and science can flourish," he added.
The past couple of years has seen frenzied activity in university finance departments to ensure their systems are ready.
The research councils have been closed during August while they convert their systems to the new full economic costing model.