Nearly a third of Scotland's universities will see their total funding cut in real terms for 2009-10.
Institutions north of the border will also receive a smaller increase in their research funding, allocated largely on the basis of the 2008 research assessment exercise, than those south of the border.
This week, the Scottish Funding Council announced how £1.14 billion allocated by the Scottish Government for 2009-10 would be spread across 20 universities. It included a main teaching grant of £663 million and £240.5 million for research. Compared with last year, total funding increased 3.4 per cent in cash terms, equating to 1.4 per cent when inflation at 2 per cent was factored in.
England saw a 4 per cent cash increase and a 2 per cent real-terms rise when inflation was included.
The universities of Stirling and Strathclyde are the major losers after the 2008 RAE. Respectively, they will see funding falls of 1.6 per cent and 0.3 per cent, despite receiving special moderation funding of £1.5 million and £1.3 million to soften the cuts.
Overall, research funding rose by 5 per cent in cash terms, better than the 4 per cent received by Welsh institutions but below the 8 per cent rise awarded to English universities.
Mark Batho, SFC chief executive, said that "at a time of economic gloom" the allocation was a reminder that Scotland had a university sector central to the country's future and one of which its people could be proud.
"There are plenty of organisations out there that would die for an above-inflation increase," he said.
He stressed that while quality-related research funding (QR) had not risen as much as in England this year, it had risen more than in England in previous years.
As in England, there were big gains for modern institutions after "pockets of excellence" in research were identified by the 2008 RAE.
The RAE 2008 showed that all Scottish universities carried out some "world-leading" (4*) research.
The Royal Scottish Academy of Music and Drama received the biggest percentage gain in research funding. Its funding was set to more than double. The Robert Gordon University experienced a 79 per cent rise in research funding, followed by the University of the West of Scotland (up 30 per cent) and the University of Abertay Dundee (up per cent).
The University of Edinburgh received the biggest increase in research funding - an extra £7.3 million (up 11 per cent) - followed by the University of Aberdeen, which received £4 million more (up 22 per cent).
The University of Glasgow, which with the University of Edinburgh represents Scotland in the Russell Group of large research-elite universities, received only an extra £500,000 (a rise of 1 per cent).
Even with moderation funding, the University of Stirling lost £1.6 million in research funding (down 17 per cent) and the University of Strathclyde £1.2 million (down 5 per cent).
How the subject areas fared
The amount of money going to some humanities areas has fallen, paralleling the situation in England. Foreign studies' funding fell nearly 29 per cent, languages 17 per cent and history 12 per cent, though arts-related topics such as media and dance gained a boost of 18 per cent.
With an extra £5 million allocated to science subjects, the biggest gains were for community-based medicine (up 102 per cent), physical sciences (up 31.5 per cent), hospital and laboratory-based medicine (up 30 per cent) and mathematics (up 18 per cent). Biological sciences funding fell 19 per cent and engineering fell 2 per cent.
The allocations were the first issued under the SFC's new grant structure, in which baseline funding is distributed through a £988 million general fund for universities (GFU) and strategic priority projects are supported via a £126 million horizon fund for universities.
A further £25.3 million in "ring-fenced grants" brings the total to £1.14 billion. Included in the GFU is the newly named £211 million research excellence grant and capital funding of £80 million.