The SNP wants to continue charging students from south of the border for higher education, even though people form other EU countries get it free, like Scots students.
Labour MSP Drew Smith told Scottish Education Secretary Michael Russell it would make the border between England and Scotland unique in Europe.
More than 3500 new English students were accepted to Scottish universities in 2013. The number of applicants from England to study in Scotland increased 14%.
Glasgow University currently charges English students £6750 a year in tuition fees.
The total four-year undergraduate fees are the same as the highest allowed in England, where charges are £9000 a year, but for a degree course that lasts three years.
Fees for medicine, dentistry and veterinary medicine are higher at £9000 a year.
Mr Smith said: "The asserted border between Scotland and England will be unique in that somehow it can break EU law preventing discrimination between member states."
Mr Russell said the policy of "objective justification" was based on the need to ensure places were available for Scottish students to prevent students from England looking over the border for a cheaper alternative.
The SNP has said if England was to change its policy on charging fees then Scotland would do the same.
Mr Russell said: "The Scottish Government believes the current practice of charging fees is the best way of achieving the current mix so students in Scotland can access education."