Medics fear there could be job losses as a result of the government's refusal to fund the research assessment exercise in full.
This would be politically disastrous for a government seeking to bring more staff into the National Health Service.
Michael Powell, executive secretary of the Council of Heads of Medical Schools, said: "Any cuts in research money to medical schools could lead to job cuts. This will have a knock-on effect on the NHS, where many clinical academics spend half their time treating patients."
Many medical schools put fewer staff in the 2001 RAE than they did in 1996. The number of research-active staff in the three clinical units of assessment fell from 5,100 in 1996 to 4,750 in the 2001 exercise.
In 1996, research-active staff in these units accounted for 10.6 per cent of research-active staff submitted. They now account for 9.9 per cent.
"As it stands, these units of assessment will automatically get a smaller percentage of the total funds available," Mr Powell said. "For medical schools, where the volume measures are huge, this could mean significant cuts in funding."
While an increased number of medical schools have achieved ratings of 5* in the 2001 RAE, and so have relatively secure funding, a number have achieved ratings of 4 and 5, and face cuts of about 15 per cent and 20 per cent respectively.
"Medical schools anticipated grades being funded in full. Those with low volume measures who didn't make it into the 5* ratings may be in particular difficulty," Mr Powell said.