But SNP ministers believe they can still charge rUK students tuition fees, keep education free for Scots and circumvent EU anti-discrimination rules by arguing that an independent Scotland would be "unique and exceptional" among EU member states.
The management fee would remain a fall-back plan, according to Michael Russell, but he conceded that it would be "extraordinarily hard to do" at Holyrood today.
The announcement cements a change in approach for the SNP in their attempt to address a projected £22 million funding gap if rUK students attain fee-free education in an independent Scotland. EU rules prohibit states from discriminating on the grounds of nationality, meaning that Scotland currently has to give fee-free education to EU students from outside the UK in order to keep education fee-free for its own citizens.
But they can impose tuition fees on students from England, Wales and Northern Ireland because the EU does regulate discrimination within member states.
If Scotland becomes independent and stays within the EU, rUK will become a separate member state and its students may then be entitled to the same rights in Scotland as other EU nationals.
Previously, SNP ministers proposed a workaround in the form of a "management fee" similar to the Republic of Ireland. But the White Paper on independence proposes an alternative approach of "objective justification", a legal term that allows states to circumvent EU discrimination rules if they can demonstrate there are legitimate reasons for limiting EU freedoms.
Mr Russell said: "The Scottish Government believes that the unique and unprecedented position in higher education of a post-independent Scotland will enable us to continue our current policy (of charging rUK students) in a way that is consistent with the principles of free movement across the EU as a whole, which is compatible with EU requirements."
Conservative MSP Liz Smith said: "On February 9, 2012, the Cabinet secretary said that he wanted to introduce a management fee for students from other EU students to defray (fund) at least some of the costs of providing free higher education. There is no mention of this policy in the White Paper, so has it been abandoned?"
Mr Russell said: "Considerable discussion took place with other countries in the EU and EU officials about the concept of management fees, and it is a very difficult thing to do. It would still be something that would be considered but it would be extraordinarily hard to do, and I think we're offering a very positive approach to the issue of EU students."