The Education Minister told the meeting in Glasgow organised by the Committee of Scottish Higher Education Principals that since an honours course in Scotland usually takes four years compared with three at an English university, "equity in my view demands that those students should pay only Pounds 3, 000 in Scotland when someone achieving a comparable qualification in England pays Pounds 3,000".
Mr Wilson has asked the Students Awards Agency to pay institutions the Pounds 1,000 for the extra year. He denies that English students who have to pay the final year's fee will be deterred or that "valuable cross-border flows" would be discouraged.
He added that of the large group of students who could be admitted as a result of their A-levels to the second year of Scottish courses only about 10 per cent take up the option. "Many more could and should be encouraged to do so. "
Mr Wilson's latest concession to Scottish students follows his earlier announcements of exemption for those who have entry deferred until next session and for those proceeding from HNC or HND college courses to university degrees.
Sir Stewart Sutherland, principal of Edinburgh University, said that differing fee levels were almost bound to be challenged in the courts. Scottish universities had to look at the structure of courses and how students fitted into them but they should also emphasise the "added value" of a Scottish honours degree when seeking employment.
Joan Stringer, principal of Queen Margaret College, Edinburgh, said that if only students from the rest of Britain were charged, that would become a legal issue.
Bernard King, principal of Abertay University, envisaged a challenge from Northern Irish students who would have to pay whereas those from the Irish Republic would not because of European Union rules. He wanted the debate widened to include maintenance costs which were a bigger obstacle to students, especially from less well off backgrounds.
Kendrick Lloyd Jones, higher education researcher for the National Union of Students in Scotland, said that students with Advanced Highers would not be excluded from the tuition fee for a fourth year because, like A-level students, they could enter second-year courses. Sir Stewart Sutherland said "a lot of water would have to flow under the bridge" if that possibility had to be dealt with.
Principals also expressed concern to Mr Wilson about the delay in publishing details of next year's arrangements for tuition fees and maintenance loans.
Richard Shaw, COSHEP's convener and principal of Paisley University, said: "The devil is in the detail and we have to be able to say to applicants, this is what it means."