A British Medical Association meeting this week heard that the funding council's research assessment exercise is "unscientific, misleading" and "pernicious".
Gareth Williams, professor of medicine at Liverpool University, attacked the exercise, which distributes research funding to universities, saying it had caused particular problems for medical schools where academics teach, research and do NHS work. Many schools have lost out financially compared to specialist post graduate institutions.
He urged medical academics to keep the issues alive, warning that many in undergraduate medical schools were "running scared".
"If a medical school scored badly in 1996 and 2001, there's a strong risk that it could say goodbye to doing research - even if there are some very good units in it."
He agreed that limited money needed to be distributed selectively, but said the problem was with the way the RAE is run. "It ignores people not funded by the Higher Education Funding Council for England," said Professor Williams. "But in my group that is 80 to 90 per cent of staff. That is typical with new groups - there are few people on full-term HEFCE contracts, so many are invisible to the RAE."
Colin Smith, chairman of the BMA medical academics staff committee, said the RAE was "pernicious" in its scoring of medical schools in its current form.
HEFCE and the Department of Health have a working group looking particularly at the RAE, medicine and health subjects.
l Students are urging medical schools to set limits on student numbers above which they say the quality of student education will be affected, the meeting also heard.
The setting of such limits will allow students or the British Medical Association to challenge levels they believe to be unrealistic or detrimental to student learning, or to call medical schools to book if they exceed the limits.
Medical schools are submitting plans for taking some of the 1,000 extra medical students the Campbell report has called for.
Daniel Atkinson, chairman of the BMA medical students committee, said:
"Many of our student representatives say their deans are planning an extra 100 students or so.
"But in those same medical schools they are already having problems maintaining quality. Students are having to sit on steps in lecture theatres and at one school there have been 16 students working with one consultant. The figure is normally between one and five."
Colin Smith, chairman of the BMA medical academics staff committee, said he thought it "outrageous" that the government was waiting before implementing the proposed 1,000 doctor increase.
He said: "We are the most under-doctored country in the European Union. But if the increase happens medical schools have to be properly funded."