Academics reacted with outrage this week to Treasury attempts to seize control of their major source of research grants by introducing a "tick-box" system to judge the value of their work.
The Times Higher has learnt that the Treasury is pushing through a "performance management delivery system" for the research councils following Chancellor Gordon Brown's ten-year investment framework for science, published in July.
The planned system will force research councils to justify the money they are given according to set performance measures. By 2007-08, the research councils will allocate some £3.3 billion to universities and research institutes.
Fears are growing in the councils that the new system could leave them at the mercy of political whim, with money being transferred to support whatever is politically important at the time.
Ian Haines, chair of the UK Deans of Science Committee, warned: "This could be the action that finally switches everyone, especially younger staff, off an academic career in the UK."
He added: "It is impossible to see how the research councils will want to support anything but safe, well-tried areas of work with guaranteed outcomes."
Although research chiefs are choosing not to defy the Treasury on this issue, senior research council officials fear a bureaucratic system similar to the research assessment exercise is about to be thrust upon them. And they worry that it will hamper efforts to fund the best research.
One senior research council figure said the Treasury had made it clear that the main purpose of the new system was to enable the Government to shift money between the councils.
The source said the Treasury was concerned that the proportion of research funding that each council received had remained fairly constant over the years.
Under the new model, councils will be expected to submit a 15-page report each year that will quantify their success in specific areas. It will include the number of publications, citations, patents and research students finishing within the period. There will also be a "light touch" review of councils every three months.
The Research Councils UK strategy group is believed to have raised concerns that these measurements will be misleading, because a researcher will usually only publish a paper two or three years after receiving a grant.
Citations take even longer to kick in.
A second research council official said: "I'm worried that we will end up with a series of tick-box indicators. I think the pressure of the process will force the civil servants to judge by numbers."
The source warned that "gameplaying would be inevitable" as each council tried to hold on to its share of the science funding pot.
They said that it might become harder to justify funding risky research or to give money to new researchers who may be slower at producing publications.
Paul Cottrell, assistant general secretary of the Association of University Teachers, said: "The last thing the academic community wants is for the research councils to become more like the RAE. What is the problem that this is supposed to be solving?"
Steve Wharton, a senior lecturer at Bath University, said: "Yet again the dead hand of government is distorting the research agenda. The research councils already do a very good job in very difficult circumstances."
The Office of Science and Technology insisted this week that all parties agreed the new system should not bog the councils down in bureaucracy. A spokesperson said it enabled the OST "to plan science investment over a longer period than the three-year spending review cycle and to ensure that resources are used to best effect".