Under new fees legislation affecting UK residents, students from Northern Ireland had been expected to pay fees of up to £9000 a year to attend Scottish universities.
However, earlier this year it emerged that if those students took up their right to dual citizenship with the Irish Republic they could apply as an EU student and have their fees paid.
While the number of students from Northern Ireland coming to Scotland is relatively small, some universities were concerned about the development.
Dundee University recorded a 20% increase in the number of students who live in Northern Ireland applying with an Irish passport.
There was also the prospect that other families with dual nationality such as Italians living in the UK could also take advantage of the loophole.
The Scottish Government initially played down the development, but officials have now decided to act.
From 2013/14 students applying to Scottish universities will be required to prove they have previously exercised their right of EU residency in order to qualify as an EU student.
The legislation will mean a prospective student has to show evidence of having lived in another EU country for a period of at least three months in order to be admitted as an EU national.
Education Secretary Michael Russell said: "Since the very recent changes to the tuition fees system there is little or no evidence of change in the make-up of applicants, but speculation over the opportunity for prospective students seeking another EU nationality to avoid paying fees has caused confusion.
"This legislation will require dual-national students to provide evidence that they have previously exercised their right of residence elsewhere and will prevent the use of dual-nationality solely to benefit from free tuition.
"We have issued guidance to universities that will ensure a consistent approach across Scotland and provide clarity for students."
Robin Parker, president of NUS Scotland, said: "We welcome clarification from the Scottish Government on dual-nationality university applicants. This will provide the guidance necessary for students from outside Scotland to make an informed choice when applying to come to university in Scotland."
Professor Pete Downes, convener of Universities Scotland, which represents university principals, said: "It's important students have access to reliable and consistent information on fees and financial support when applying to university in Scotland and we trust the forthcoming legislation will provide exactly that.
"Scotland's universities have not seen a large influx of applicants from Northern Ireland looking to exploit the loophole, but it is necessary to take action to close it for future years to avoid any confusion for students and parents alike."
In accordance with Scotland's EU treaty obligations, the nationals of another member state must be treated in the same way as students living in Scotland.
Scottish students benefit from free tuition, whereas students elsewhere in the UK do not. This gives incentive to students from elsewhere in the UK who can claim dual nationality to do so in order to apply to Scottish institutions as a non-UK EU national and so obtain free tuition.
The number of students with Northern Ireland postcodes accepted to Scottish institutions for 2012/13 is down by 19%, according to official statistics. Equivalent figures for students with Republic of Ireland postcodes are down by 6%.
Liz Smith, education spokeswoman for the Scottish Conservatives, said: "For 18 months the Scottish Government has had its head in the sand over the dual nationality issue and, for some inexplicable reason, has been unwilling to remove the confusion over who has to pay fees and who does not."
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