Universities UK, the umbrella body for vice-chancellors, is struggling to represent the interests of all its members since publication of the higher education white paper, according to some academics.
There are already lobby groups representing different interests, such as the Russell Group, the Coalition of Modern Universities and the 1994 Group.
Michael Driscoll, vice-chancellor of Middlesex University and the next chair of the CMU, said: "The white paper has put a wedge between a very few universities and the rest of the sector. At least two-thirds of universities are going to have no access to significant research cash and this makes it hard for a membership organisation such as Universities UK.
It has to acknowledge differences."
He said that UUK had coped well with devolution through the establishment of Universities Scotland and Higher Education Wales.
Professor Driscoll thought UUK might end up with a federal structure. This idea had been raised within the UUK in the past.
Fifteen of the 36 members of the CMU responded to a THES questionnaire on the white paper. Nine expressed doubt as to whether UUK could continue to represent all universities. A similar number said the white paper would create a two-tier system. About half said the new research framework would damage their university, with a few undecided.
Geoffrey Copland, current chair of the CMU and vice-chancellor of Westminster University, said: "Bodies such as the CMU come together when there is a common interest - and clearly on the stratification of research there is common ground. But this concern goes wider than the CMU."
Professor Driscoll said: "We have already had constructive dialogue with members of the 1994 Group."
Alasdair Smith, chair of the 1994 Group and vice-chancellor of Sussex University, declined to comment on the role of UUK but said the research framework outlined in the white paper created problems for his group. "The 1994 Group consists of universities that are excellent in research but are not large. We are therefore concerned that the higher education strategy paper seems to say that 'big is better'. That is not necessarily true."
The Russell Group welcomed the white paper but said that details were not yet clear.
A UUK spokesperson said: "We are proud of the fact that the UK has a diverse and vibrant university sector.
"There are, and will remain, many areas of common agreement and we will continue to work together on these."