The most contentious proposal is to abolish fees for Scottish students in Scotland, while Scots studying elsewhere in the United Kingdom will continue to pay fees.
A Scottish student is one who was living in Scotland when an applicant; having a granny with a Highland home, or residence during a Scottish course will not count.
The Scottish Executive claims its hands are tied by European law. Nicol Stephen, depute minister for enterprise and lifelong learning, said: "What we only received advice on once we had the structure of a final agreement was that if you paid the tuition fees of Scottish students attending English or Welsh universities, an European Union student could claim equal treatment and we could end up having to find the money for a student from Rome studying at Cambridge."
This could potentially have led to the Department for Education and Employment reclaiming Pounds 20 million from Scotland.
John Usher, director of Edinburgh University's Europa Institute, said that in the 1980s higher education access conditions, notably fees, were held to fall within the scope of European Community law, with the result that discrimination was prohibited.
"EU students at Scottish universities cannot therefore be charged fees if Scottish resident students are not charged fees," he said. "If the Scottish Executive were to pay the fees of Scottish resident students at other UK universities, discrimination against students from other EU countries could be eliminated only by offering them the same treatment.
"On the other hand, reverse discrimination against a member state's own citizens does not appear so far to have been treated as a breach of EC law."
Students have renewed their call for tuition fees to be abolished across the UK, while the Committee of Vice-Chancellors and Principals has warned that any change in Scottish funding arrangements must be monitored for its UK-wide impact on student movement.
"It is crucial that no student is put off attending the university or college of their choice by any differential funding arrangements," said CVCP chief executive Diana Warwick. "UK universities offer a huge wealth of excellent degrees in different specialist areas and these should be open to anyone who can benefit from higher education, whatever their circumstances and wherever they are from."
The Scottish Conservatives' education spokesman, MSP Brian Monteith, said applicants would now need an accountant as well as a careers adviser.