In a submission to the Scottish Parliament’s education committee, Universities Scotland said a yes vote would “inevitably” lead to more students heading north of the border in search of free tuition.
At present, Scots are exempt from fees in their home country, while those from elsewhere in the UK pay up to £9,000 a year.
However should there be a yes vote in the referendum, rUK (rest of UK) students would be classed as EU citizens and therefore entitled to the same free tuition as Scots.
Universities Scotland, which represents university principals, said: “Universities Scotland believes it is essential that a regime is in place to ensure sustainable management of cross-border flow on a stable and predictable basis. This is important as part of any constitutional outcome of the referendum, whether this is independence or further post-referendum development of the devolution settlement.”
It said that otherwise the fee differential between England and Scotland would “inevitably lead many more English students in particular to make the economically rational choice to study in Scotland.”
And it warned that would lead to a “significant displacement” of Scots who would normally study in their home country.
“If there is a vote for independence, we believe it is essential that prior to independence day the Scottish Government is able to give institutions robust legally-defensible certainty that a regime will be in place which enables a sustainable level of cross-border flow,” it said.
Figures released by the Scottish Government under Freedom of Information legislation show that if even 10 per cent of rUK students choose Scotland in the event of a yes vote, then those studying in their home country would be likely to miss out on places.
Earlier this year, education secretary Mike Russell warned of an influx of “fee refugees” should the EU prevent Scotland charging UK students fees following independence.