Engineering and medical researchers voiced fears this week that the "new-look" research assessment exercise would do little to protect their disciplines from further funding cuts.
The Higher Education Funding Council for England last week issued the first details about how the reformed RAE will work in 2008, promising fair treatment of all types of research and an end to game-playing in the sector.
But both the Royal Academy of Engineering and the British Medical Association remain unconvinced that the old problems affecting their disciplines will disappear.
At a meeting with engineering panel chairs, Hefce representatives and key industry players on Monday, members of the RAEng questioned whether the new exercise would give enough credit to applied research.
Phil Ruffles, vice-president of the academy, said this was a crucial issue as it was now normal for the best university engineering departments to carry out at least half of their research for industry.
The academy warned Hefce that the traditional use of citation rates as a measure of research quality did not work for a practice-based discipline such as engineering.
The BMA demanded this week that additional measures be taken to prevent further downgrading of medical research in the 2008 RAE.
It issued a paper warning that RAE panel members had largely given lower ratings to medical disciplines than to non-medical subjects such as veterinary science. It says that the current RAE is biased against medics in areas such as surgery or obstetrics and gynaecology, whose research output is often lower due to their heavy clinical workload.
Michael Reiss, chair of the BMA medical academics committee, said: "We are seriously undervaluing the strength of medical research and therefore we are seriously underfunding it."
Hefce insisted this week that it had meetings with both the RAEng and the National Health Service research directorate to ensure that excellence in both engineering and medical research is fully rewarded in the forthcoming RAE.
Rama Thirunamachandran, director of research at Hefce, said: "In both cases users will be members of panels to ensure that the full significance of applied and practice-based research is measured."