Universities keen to be seen as research intensive are fighting to keep their nursing academics out of the numbers submitted for the research assessment exercise. Nursing was the worst performing subject in the last RAE.
Funding councils use the RAE to assess how much money each university receives for research.
In April, the Higher Education Funding Council for England wrote to universities saying that those that had excluded staff on academic-related contracts - which apply to many nursing staff - had to resubmit.
The bulletin said that some universities had "raised concerns that they might be disadvantaged by applying the RAE guidance strictly if others do not do the same".
A number of universities are challenging the clarification.
The dispute focuses on the percentage of staff deemed research active. If more than 95 per cent of academic staff in a subject area, or unit of assessment, is research active, the unit is awarded an A.
This goes down to F if less than 20 per cent are research active. These letters do not have a bearing on funding but can affect a university's position in newspaper league tables.
The Hefce bulletin said: "The effect of not including some staff in the count would be artificially to inflate the proportion of staff returned as research active."
A spokeswoman for Leeds University, which has excluded certain staff, described the Hefce clarification as a "reinterpretation of the system".
"It runs against long-established practice," she said.
Richard Masterman, director of research policy administration at Nottingham University, which has excluded staff, said: "We are looking at the implications of the bulletin."
He said that the matter had not yet been resolved and was not sure if his university would have to resubmit.
But Martin Snaith, pro vice-chancellor for research and staffing at the University of Birmingham, said: "We have been absolutely scrupulous in including our nursing staff in our RAE return. It means that certain departments will be awarded a letter C rather than a letter A... It is important that all returns are submitted following the same rules."
- Universities have been more selective in choosing who to include in their submissions to this year's RAE.
The number of pieces of work submitted has fallen by 5 per cent compared with the last exercise, held in 1996. The number of staff submitted is fairly static but the eligibility criterion has changed: institutions can claim the work of staff who left after March 31 2000.
Taking this into account, the number of staff submitted has also fallen by about 5 per cent.