Critics have warned that the abolition of the Scottish Funding Council could pose a threat to academic independence.
The concern follows a decision two weeks ago to put the Scottish government's economic agencies under a single national board.
It has since become clear that the four boards of directors running the agencies face abolition.
Enterprise Minister Keith Brown ordered the review of Scottish Enterprise, Highlands and Islands Enterprise, Skills Development Scotland as well as the Scottish Funding Council.
He concluded that a national board should be created to oversee the different agencies and ensure their work was "aligned".
A Scottish government spokesman said there was no timetable for the changes.
He also confirmed that details had to be worked through, including the question of whether a government minister will be chair of the national funding board.
The move is the second phase of reform for the economic agencies, which began after the Holyrood election in May.
What has since become clearer to those who work for the agencies is that the boards that govern them face abolition some time after the national board is set up.
The boards have not been formally notified of this but have been told in private meetings.
There is concern within the Scottish Funding Council that the implications for academic freedom have not been thought through.
The funding council was set up in 2005 to replace separate boards for higher and further education.  It oversees allocations of government grants for universities and colleges.
Alastair Sim, chief executive of Universities Scotland, said he would be looking for details of how the new national board would work.
He said: "One particular interest is ensuring that the Scottish Funding Council retains its much valued role as an expert body at arm's length from government, while working collaboratively to help boost Scotland's innovation and productivity."
Prof Iain Gray, vice-president of the Royal Society of Edinburgh, the academic institute, said universities were in favour of measures that would improve links with business.
But while university research remains one of Scotland's biggest strengths, he said there was a need to explain the Scottish government's strategic approach to innovation in the economy.
He said: "We need to get a clear strategy, and avoid unintended consequences of bringing together organisations with different remits, without thinking things through."
Scotland spends a lot more per head of population on economic development than the rest of the UK. But is it getting value for that money? Is it really helping drive growth?
The lack of data on that seems to have been one of the driving forces behind the review of enterprise agencies.
But even some of those close to the heart of the review process have been puzzled as to what the minister, Keith Brown, has been trying to achieve.
His conclusion, published in October, was largely supportive of what the agencies have been doing.
That's while it identified opportunities to improve co-ordination and alignment, tackling duplication and improving economic data, notably on the requirements of the labour market.
The biggest threat the review appeared to pose was to the autonomy of Highlands and Islands Enterprise.
Yet rather than being absorbed, it was taken as the model for a similar agency covering the south of Scotland (its boundaries are yet to be decided).
However, if there is to be one board covering all these agencies, and the existing boards are to be abolished, it is not clear how the agencies will or can remain distinctive in their regional roles. Critics are likely to portray this as centralisation.
The odd one out in this is the Scottish Funding Council, which has the politically sensitive role of allocating funds while protecting universities from undue political interference in their academic work.
It is under instructions to get a better link between the university sector's many strengths and the economy.
But it also has a role of protecting the universities in studies and research which do not have direct economic impact.
The sensitivity of that role would be harder to protect under a national board largely concerned with the economy - and above all, if it turns out that the cabinet secretary is to be the one with the key role of allocating which universities and which departments get the most favourable funding.
As with much of this reform programme, that's not clear.
Concerns have been raised about the centralisation of funding for Scottish universities, BBC Scotland has learned.