Concern has been sparked because, from next year, universities in England no longer face restrictions on the number of students they can recruit.
That means there could be fewer students from the rest of the UK (rUK) seeking to secure a place at a Scottish university.
RUK students - who pay fees of up to £9000 a year - were expected to provide a vital new source of revenue for universities north of the Border, but if institutions fail to recruit enough they could be facing a funding deficit.
Universities Scotland, which represents university principals, has raised the issue with the Scottish Parliament's education committee. The body said that, by the end of 2015/16, the withdrawal of public funding for rUK students will be all but complete, with the sector having lost some £92 million.
A spokeswoman added: "The removal of the student number cap in England will make it more difficult for institutions to sustain rUK student numbers."
Gordon Maloney, president of student body NUS Scotland, echoed the warning. He said: "The uncapping of student numbers down south could put further pressure on numbers in Scotland.
"If Scottish universities are worried about the number of students coming here, then they need to seriously consider their fee levels, the financial support they offer and do more to promote fair access for all students, regardless of which country they're from."
The issue has arisen at a time when Scottish universities are already struggling to recruit rUK students.
It was revealed earlier this year that more than half of Scottish universities attracted fewer students from the rest of the UK after the introduction of fees of up to £9000.
Institutions that saw a decline included Abertay, Dundee, Edinburgh Napier, Glasgow, Queen Margaret, the Royal Conservatoire, Strathclyde and University of the Highlands and Islands.
Overall, numbers of rUK students coming to Scotland increased by 5% between 2011/12 and 2012/13, but Edinburgh University was responsible for most of the rise. Last year, Chancellor George Osborne announced that a cap on the numbers of students England's universities can admit is to be lifted in 2015.
The change means universities will be able to expand further, should they wish, with the potential to admit an additional 30,000 students in the first year.
Meanwhile, in a separate submission to the education committee, which is looking at the impact of independence, David Raffe, from the centre for educational sociology at Edinburgh University, called for different parts of the UK to work more closely together whether independence happens or not.
He said: "The ideal of the UK as a partnership suggests that it provides the context in which to resolve the conflicts and tensions that arise from this interdependence. This has not happened. Successive reports have criticised the inadequate arrangements for co-ordinating government policy across the four home countries.
"The failure of policy co-ordination among the UK partners is reflected in the fee increases in England in 2006 and 2012. These were introduced with minimal consideration for, or consultation with, the devolved governments, but they have dominated their subsequent policy agendas."