Phil Shiner, of Public Interest Lawyers, is reportedly preparing to argue that the policy breaches discrimination rules under the European Convention on Human Rights, and may also breach the UK Equality Act.
Under EU rules, governments are not allowed to discriminate against students from any other EU state. Scotland is not an EU state but a region within the UK.
The Scottish Government maintains that EU rules do not apply to different policies within member states.
A Scottish Government spokeswoman said: “We are clear that the proposals set out are lawful. Tuition fee arrangements are based on ‘ordinary domicile’ not nationality.
“In an ideal world, no students would pay fees. Our main priority has to be to protect opportunities for Scottish students to study at Scottish institutions by maintaining free education north of the border.
“With the UK Government introducing tuition fees south of the border of up to £9,000 per annum, Scottish students studying in England will continue to receive financial support in the form of bursaries and loans.”
The spokeswoman added that there was no record of any correspondence by Mr Shiner regarding his challenge.
The Scottish Government is also trying to find a way to charge students from the rest of the EU.
One option that has been suggested is to charge EU students a “service charge” similar to Ireland.
Scottish Tory education spokeswoman Liz Smith said: “This is yet further proof of the shambles which is the SNP’s policy on higher education funding.
“I am not in the least bit surprised to hear there will be a legal challenge as there is a clear issue of discrimination against students from the rest of the UK, setting them apart from students from Scotland and the EU.
“This is grossly unfair to these individuals as well as a threat to the excellent reputation of our universities.
“It is also likely to distort the university admissions process. If Scottish universities have to look to fee-paying students in order to obtain greater income, then it sends a clear message that financial considerations matter more than academic merit.
“This problem is entirely the fault of the SNP Scottish Government. By refusing to admit the true extent of the funding gap, the SNP is damaging the future of our university system.”
Mr Shiner is also acting on behalf of two English sixth-formers who were granted permission to challenge the UK Government’s plans to triple tuition fees in the High Court.
A judge ruled in June that the two students have a case against the increase and should be given a full hearing.