The Scottish education secretary is asking universities to question the need for four-year degrees in an attempt to cut costs, Times Higher Education has learned.
Mike Russell, secretary for education and lifelong learning in Scotland, has held a series of one-to-one meetings with university principals to consider the future of the sector.
The Scottish National Party remains committed to free higher education, but this has led to fears that the Scottish sector will not be able to keep pace if the cap on tuition fees is raised south of the border.
The issues under debate in the meetings held by Mr Russell have included a consideration of whether Scottish universities still need to offer a four-year qualification.
It is understood that the education secretary floated the idea with the principals of some post-1992 universities, who are seen as more progressive, but not with other heads.
This has led to speculation that the Scottish government could favour a more diverse higher education sector, with different institutions delivering different kinds of degrees.
The government confirmed that a series of meetings with university principals had taken place as part of an "ongoing dialogue with the sector".
"All sensible views and ideas are being encouraged in those ongoing meetings ... the sector as a whole must look creatively at the potential challenges posed by any changes in the fees regime south of the border," a spokesman said.
Questions over whether the four-year degree should continue were met with anger by some academics, who raised fears that Scotland's unique offering could be eroded.
Mary Senior, Scottish official at the University and College Union, said it was "astonishing" that any major structural changes should be discussed on an individual basis with principals rather than openly, with the sector as a whole.
Neither UCU Scotland nor Universities Scotland has had a formal meeting with the minister.
"We have always maintained that any change to the four-year degree must be for sound educational reasons, not for the financial expediency that the government seems to be discussing behind closed doors," Ms Senior said.
"We expect an SNP minister to understand the value and distinctiveness of the Scottish educational system. We hope he is not proposing to replace it with an English model that is out of step with the rest of Europe."
Opponents of changes to the four-year degree argue that a programme with two general and two specialised years is superior to England's three-year structure.
They add that that Scottish system also made it easier for students to spend a year abroad, and fits into the Bologna Process.
A spokesman for Universities Scotland said: "We recognise the tight financial climate ahead and that universities have to be creative in finding ways to deal with it."
"In turn we will be encouraging the cabinet secretary to recognise just how important to Scotland its universities are, and to make a strong case to cabinet for a level of funding that will not irreparably harm one of Scotland's most important assets."
The spokesman said the four-year degree was a "standard" across Europe and an important part of Scotland's tradition, adding "we would need to be very confident that any changes ... would not do more harm than good".