The funding council is to mount a political defence of the £1.4 billion it allocates for universities' research each year - amid concerns that the money could be at risk if its purpose is not clearly set out.
A paper presented at a recent Higher Education Funding Council for England board meeting, published online this week, attempts to set out a case to protect, in the longer term, the QR research budget. QR funding is distributed to universities to fund blue-skies research, based on the results of the research assessment exercise.
The paper, The Role of QR in the Research and Innovation Landscape, cautions: "We would see risks to the council's reputation and to the prospects for our grant in future if we do not develop a clear strategy for making known our policy in this field and for encouraging higher education institutions to make the best use of our grant in coming years to deliver national policies for innovation."
The Government's decision last year to create the Department for Innovation, Universities and Skills brought together control of both strands of the so-called dual-support research funding system - Hefce's QR budget and the budget of the seven research councils.
The fact that both strands are within one Whitehall department could make it easier to create a single funding system, observers have speculated, despite government reassurance that dual support is safe.
Hefce's paper says that the creation of the new department - along with the recent publication of the DIUS White Paper Innovation Nation - has "thrown into relief" some questions about QR that would be "timely to consider".
It says that Hefce should argue that the central achievement of QR lies in enabling universities to invest in their infrastructure, train new researchers and identify and invest in new areas of work. Hefce "should be quite clear" that the research councils' funding will achieve its "best effect" in tandem with QR.
"The research councils increasingly fund against thematic priorities: to deliver on these into the future institutions will require the support of QR to maintain the breadth and depth across the entire research base to be ready and able to respond quickly and effectively to new priorities as these emerge," the paper says.
"Baseline funding through QR enables institutions to apply for research council funding - including supporting the preliminary thinking and research required to generate high-quality proposals," it says.
Top researchers typically take research council grants with them, so QR provides "continuing support" for universities to keep up their activities in areas where they have lost researchers.
Steve Smith, vice-chancellor of the University of Exeter, said there was no reason to think ministers had any plans to scrap dual support but that "did not mean" there were not "deep issues" about the future of QR. "We have to be clear what purpose it serves," he said.
Bahram Bekhradnia, director of the Higher Education Policy Institute, said research councils were also engaged in a similar process of trying to "make clear to their paymasters" what was distinctive about their funding.