Ferdinand von Prondzynski, principal of Robert Gordon University in Aberdeen, believes 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 reduction in 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%.
Mr von Prondzynski said: "We know that high value research produces development and growth, but what do we conclude from this?
"The most common, but in some ways also the most politically lazy, conclusion has been to go for what is known as research concentration, under which an ever smaller number of institutions and of researchers are allocated public funding.
"This will tend to shift investment to older city locations hosting older universities. It is also unhitching research funding - from any link with local development needs."
Mr von Prondzynski, the chairman of a recent commission on university governance, said the shift could have repercussions for the economy.
He said: "Research concentration in Scotland, if done on this basis, will tend to undermine any economic development policy that the Scottish Government may have in mind.
"First, research would be almost entirely restricted to the central belt. Secondly, it will tend to reflect the priorities of the universities in question, which in turn will have little connection with Scottish national priorities."
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 Research Excellence Grant, no longer funding lower-graded research and concentrating instead on work that ranks highest in international comparisons.
At the time, lecturers' union UCU Scotland said the development could create a two-tier system with some universities doing very little research – to the detriment of students.
However, Mark Batho, chief executive of the SFC, said funding for university research had increased by £10m for the next academic year.
He said: "We concentrate our funding to support the best quality research and to lever the greatest amount of resource from other research funders.
"The recent establishment by a global pharmaceutical company of a new fund to support SFC-funded research in life sciences is one example of how that equation works to the benefit of Scotland.
"Along with universities and other public bodies we continue to invest in ways to translate high-quality university research into new jobs and economic growth for Scotland."
A Scottish Government spokesman said: "Scotland has a number of avenues available to fund research beyond our higher education sector.
"For example, Scottish Enterprise provides grants of up to £100,000 through the Smart Scotland programme and research and development grants.
"Both these initiatives support hundreds of Scottish firms each and every year."