The Government insists that higher education institutions could continue to charge students from England, Wales and Northern Ireland fees of up to £9000, while at the same time offering free tuition to those from north of the Border.
But last month, the European Union's governing body said the plan had no precedent in the EU and could be regarded as "a covert form of discrimination on grounds of nationality".
A legal challenge to the policy is likely after a Yes vote, which commentators say could take years to resolve.
Universities are also concerned a legal challenge could be directed at them rather than Holyrood ministers.
A submission to Holyrood's education committee from sector body Universities Scotland calls for more detail before March 24, 2016, when the country would become independent following a Yes vote in September's poll.
It states: "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 that enables a sustainable level of cross-border flow."
Commenting on the independence White Paper, the submission adds: "We look forward to seeing a full articulation of the Scottish Government's proposed objective justification as soon as this is developed."
A Government spokesman said: "The requirements of the EU allow for objective justification - that is clear evidence of exceptional circumstances. This is explicitly acknowledged on page 199 of Scotland's Future where it expressly identifies objective justification as the basis of our approach. This is a point also made in independent legal advice sought by Universities Scotland.
"The Scottish Government will ensure that clear arrangements, fully compliant with EU law, are in place."