Fears have resurfaced about the future of the dual-support system for research as the government seeks formal advice on how to carve up the science budget.
Six organisations have been asked by the Department for Business, Innovation and Skills for advice on how to spend the budget.
They are being invited to comment specifically on the split between the research council-controlled cash and the quality-related research (QR) funding pot - the two arms of dual support.
QR funding is distributed via a block grant from the funding council. It pays for curiosity-driven research and is allocated on the basis of the research assessment exercise results.
The research councils, in contrast, distribute their funding competitively, and increasingly in line with thematic priorities.
The research council budget comprises the lion's share of the £4 billion annual ring-fenced science budget, while QR funding totals about £2 billion annually.
Importantly, the two funding streams have in the past been treated as separate pots by government.
However, there has been concern since the budgets came under the same departmental umbrella in the former Department for Innovation, Universities and Skills, and now BIS, that research funding could leak from QR to the research councils.
This would result in universities having less freedom to spend research funding as they wish, with more of it directed at specific projects.
In an interview with Times Higher Education, Adrian Smith, director-general for science and research at BIS, revealed that the QR component was now in effect being wrapped into the science budget.
"The big picture is that we are making decisions about both (research council and QR funding), so that is what we mean when we talk about the science budget," he said.
"It is illogical not to consider that whole lot because that is the public-sector research investment that goes into universities."
Nick Dusic, director for the Campaign for Science and Engineering, said the fact that the two components now sat so closely together was "big news".
He said it raised questions about whether the science ring-fence now applied to QR funding as well.
A BIS spokeswoman said that while the science budget and the higher education research budget were both now controlled by the Science and Research Group within BIS, headed by Professor Smith, the science budget was protected by a "parliamentary ring-fence" while the higher education research budget had an "administrative ring-fence".
She said Treasury approval was required before funds were transferred from the latter.
Professor Smith said he had asked the six bodies participating in the formal consultation to advise on how the science budget should be allocated in the three years after the current Comprehensive Spending Review period ends in 2010-11.
The groups being consulted are the Royal Society, the Royal Academy of Engineering, the British Academy, the Council for Science and Technology, the government's departmental scientific advisers and the CBI. Universities UK has not been asked to participate.
THE understands that the groups are first being invited to advise on issues such as how research funding should be split between the two arms of dual support, and whether any cuts should be made across the board or if certain priorities should be protected.
Later, when the overall allocation is known, the groups will be invited to advise on specifics of where any potential cuts should be made. Their advice will be published.
One senior source from a group involved in the consultation said that the participants feared being left "carrying the can for the painful cuts that may be coming down the line". He said: "I think the tension is going to be felt by almost all."