Lecturers and students have criticised cuts to the research budgets of newer universities, stating they could lead to a two-tier system of university education in Scotland.
The attack comes a week after Ferdinand von Prondzynski, principal of Robert Gordon University, in Aberdeen, said the move could undermine the Government's wider economic strategy.
In 2012/13, newer universities such as Abertay in Dundee, Edinburgh Napier, Glasgow Caledonian, Queen Margaret in Edinburgh, and Robert Gordon will all see a cut to their share of Scotland's research budget – an annual fund of £233 million.
At the same time, research investment at traditional universities such as Glasgow, Edinburgh and St Andrews will increase, in some cases by as much as 6%.
Mary Senior, Scottish official of the UCU, which represents lecturers, said: "We believe research funding should build a research base in all institutions, as the concept of research-based teaching is fundamental for the development of our universities.
"We are clear that the moves towards a two-tier system of research or teaching universities in Scotland undermines the concept of research-led teaching, and devalues the essential and very useful research that is pioneered in the newer universities such as Queen Margaret, Glasgow Caledonian and Robert Gordon."
Robin Parker, president of student body NUS Scotland, added: "We would be very concerned if research became too concentrated on only a few universities in Scotland.
"Students wouldn't accept a two-tier university system in Scotland, where older institutions receive almost all of public research funds, leaving our newer universities with little research activity.
"This would harm the student experience, and harm these institutions too. One of the things that make universities what they are is that they conduct research and link that to their teaching. This is a crucial core activity and so we would not accept any move away from this."
A spokesman for the Scottish Funding Council, which distributes research funding on behalf of the Government said: "We support research in all of Scotland's universities through the allocation of the Research Excellence Grant (REG).
"This funding underpins the research base in Scotland and is intended to help our universities to secure additional research support from the research councils, the major research charities, the European Commission and from business and industry."
A Scottish Government spokesman said: "We are committed to maintaining Scotland's position as a world-leading research centre.
"Scottish universities regularly successfully compete for research funding from a range of sources, including from the EU and research councils.
"In addition, funding for the REG increased in 2012-13 by £10m to £223m."
Concentration of research funding was first highlighted in the Scottish Government's Green Paper on higher education, published in 2010.
This was followed up in September last year by a letter of guidance to the Scottish Funding Council (SFC) from Michael Russell, the Education Secretary, highlighting his priorities between 2012 and 2015.
He said: "To ensure Scotland's research remains internationally competitive, you should continue to focus on world- leading and internationally excellent research."
The SFC has now changed the way it allocates its REG, no longer funding lower-graded research and concentrating instead on work that ranks highest in international comparisons.
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