The Royal Society is calling for the government to scrap the research assessment exercise in favour of a "profile-based system".
Increases to the selectivity of research funding will have "serious detrimental consequences" for science, the society warns this week in its response to the higher education white paper.
It stresses the need to develop a more stable underlying structure for higher education. It wants the government to recognise that it is individuals and not departments that undertake research, and that excellent researchers should be supported regardless of location.
John Enderby, vice-president of the Royal Society, said: "The level of research funding at both departmental and institutional levels is already highly selective and should not become more so."
The society disagrees with the introduction of 6* departments. And the submission raises concerns about cuts to 4 and 3a-rated departments. It says many universities will become unattractive to high-quality staff, and that the lack of funding will cement the spread of 5 and 5* departments.
The submission also argues that demand for higher education might be reduced by the introduction of differential fees and that it may take longer than anticipated for institutions to benefit.
The society is concerned that debt might prevent graduates pursuing postgraduate studies.
• The new professional body for librarians has accused the white paper of failing to acknowledge the role of libraries in learning, writes Olga Wojtas.
The Chartered Institute of Library and Information Professionals supports the paper's recommendations, but warns that there is not enough recognition of the important contribution made by academic-related staff. It adds that information literacy should be added to the list of core skills.