The Scottish Higher Education Funding Council will hold a special meeting on January 11 to draw up its funding advice to ministers. But there is speculation that there will be no final decision until next year's grant letter is issued in March.
Scottish research has improved by 18 per cent since the last research assessment exercise, compared with a 15 per cent improvement in England.
Lord Sutherland, convener of Universities Scotland, has called for a "research escalator" that would increase funding by 20 per cent annually for the next three years.
Shefc had warned that a rise in research quality was likely to mean an end to funding 3-rated departments, but this has come under fire from the Scottish Parliament's enterprise and lifelong learning committee. It says this would hit new universities, whose research is potentially crucial to the economy, and would have a knock-on effect on their teaching of 35 per cent of the sector's students.
Committee convener Alex Neil said the RAE results proved the committee's point. "The excellent research being produced in Scotland's universities is not confined to a few particular institutions."
Bernard King, principal of the University of Abertay, Dundee, said new universities had achieved many 3as and 4s since the last RAE without the levels of funding enjoyed for decades by traditional universities. This raised questions of value for money, he said.
Ian Johnston, principal of Glasgow Caledonian University, said some key areas, such as nursing, had 3as, and it would be absurd not to fund centres of excellence in these subjects.
Shefc makes no funding distinction between 5 and 5*.
* Welsh higher education is preparing for a shift in research funding priorities, following "resounding success" in the research assessment exercise.
With the number of Welsh departments receiving a 5* rating quadrupling since the last exercise, the redistribution of research wealth is expected to be even more marked than in England.
The Welsh higher education funding council will not make any final decisions on research funding until its council meeting in February. But a policy decision has been made in principle to fund 4, 5 and 5* departments at levels comparable with the rest of the United Kingdom.