The Treasury is keen to use a new metrics-based research assessment system that would further concentrate research funding, potentially creating a top tier of no more than ten institutions, vice-chancellors claimed this week.
Universities have spent months wrangling over what sort of metrics should be used to judge the quality of their research, having roundly rejected all five models put forward by a government working party in June.
But senior figures warned this week that by concentrating on process, the sector was missing the political intentions behind a drive to replace the unpopular research assessment exercise.
One vice-chancellor at a leading research university said: "I've always feared that there are bigger issues at play here, such as pot size and research concentration.
"The Department for Education and Skills thinks that funding should be largely concentrated between 25 universities, but the Treasury thinks it should be ten. The Treasury is much more wedded to concentration."
Another prominent vice-chancellor said: "The Government believes in selectivity. But the question is, where do you set the line? There will be more concentration under metrics."
But Steve Smith, vice-chancellor of Exeter University and chair of the 1994 Group of smaller research institutions, said: "The job of metrics is supposed to be to mirror the current distribution of funding. If it is about excellence, we have nothing to worry about."
Institutions with an arts bias remain anxious that the Treasury wants to use metrics to shake up the balance of funding between subjects. Geoff Crossick, warden of Goldsmiths, University of London, said: "There is real concern about the shifting size of subject pots. If it produces a shift away from non-science subjects and towards science that would be a real problem."
Research-intensive universities have been careful to sing from the same hymn sheet in their responses to the government consultation, calling for a basket of metrics and a serious peer oversight element. Professor Crossick said: "The important point is that the 1994 Group and the Russell Group are both backing the same critical principles here. When all the top 40 institutions say this is the way to go, it is hard for the Government to go against it."
University chiefs close to Westminster said that key Treasury figures had made clear their desire to distance themselves from the five original metrics models - and the furore they sparked - as quickly as possible.
One vice-chancellor warned: "They are losing patience. They are growing tired of a sector that moans about the RAE at every cocktail party, then holds on to it like a comfort blanket when they try to change it."
Another vice-chancellor from a high-profile institution said: "Everyone was telling the Government that the RAE had to go and that metrics were the way forward. The Royal Society went on about it for years, as did many universities. Then the Government decides to introduce metrics and all hell breaks loose. I think it feels very annoyed about conflicting messages."
Yet the head of one research-intensive university said: "The Treasury should be a little more careful about where it finds its evidence. Despite the denials, the fact is that it spoke to a very small number of people about what to do. Had it talked to more people it would have been more cautious."
Eric Thomas, vice-chancellor of Bristol University and chair of Universities UK's research strategy group, said: "We split the atom - surely we can sort this out? I see no a priori reason why a basket of metrics cannot be constructed that will allow research funding to be distributed fairly."