The number of European Union students at Scottish universities rose by 7 per cent in 2011-12, from 16,310 to 17,475, figures published by the Higher Education Statistics Agency have revealed.
Over the same period, the number of enrolments of UK-domiciled students dropped by 4 per cent.
Scottish Labour's shadow education secretary, Hugh Henry, claimed that the figures showed Scotland was facing a "ticking timebomb" in terms of future EU subsidies.
"If Scotland decides to separate from the UK, the costs of free tuition for EU students will rocket to more than #163;225 million as students from the rest of the UK become eligible for free tuition here," Mr Henry argued.
A spokeswoman for the Scottish government said it was making a further 2,000 places available for Scottish students in 2013-14 and would continue to work with universities to continue to ensure Scottish students have access to the opportunities they need.