Universities are cutting the number of PhD places in their weaker departments, raising fears of academic job losses as the demand for doctoral supervisors declines.
Faculties rated below 4 in the research assessment exercise will have their funding council cash for training doctoral students withdrawn from this month.
The decision, made by the Higher Education Funding Council for England, has sparked a debate about whether in future there will be enough academics in the subjects worst affected. These include education, engineering, computer science, business and management.
One education researcher in a 3a-rated department at a pre-1992 university described the changes as "criminal".
He said that despite his department having more PhD students than any other in his university, there were no signs of the institution offering central support. "It will have a devastating effect on us and on education generally.
"I have 16 years of experience supervising PhD students, but now I'm not allowed to continue unless I can attract research funding myself. How are we supposed to do good-quality research to develop learning and teaching in schools?" he asked.
The researcher said redundancies were expected as a result of the changes but academics were afraid of speaking out.
John Anchor, head of business studies (rated 3b) at Huddersfield University, estimated that in his department the number of PhD places could drop from 38 to 25.
He said: "I am quite concerned that opportunities are going to be lost for students who want to do PhDs here and for the academics who want to supervise them.
"Just because a unit of assessment gets a particular score in the RAE, it doesn't mean there aren't very well-qualified and appropriate PhD supervisors there."
Alistair McCulloch, head of research at Edge Hill College of Higher Education, believes the cuts will have a detrimental effect on UK plc. He said: "We are talking mainly about vocationally oriented courses. This is going to reduce numbers of highly skilled professionals in these disciplines and reduce opportunities for further study in these areas as well."
Professor McCulloch, who is a member of the UK Council for Graduate Education's Executive, said part-time PhDs would be worst hit. This would threaten the widening participation effort and the Government's aim to raise skills nationally.
He has calculated that more than half of part-time general engineering PhD places could go, together with almost half from business and management and a third from computer science.
"The institutions that will be particularly affected often serve their local communities and industries, rather than the international market," he said.
But not all the UK's estimated 500 departments rated 3a or below will lose out. In March, the funding council announced that "emerging subjects" such as nursing and sports-related studies would continue to receive PhD support. There will also be "transitional funds" for departments that are to have cash withdrawn.
Some universities will divert money from other areas to save PhD places.
Others will register students in higher-rated departments as a short-term measure.