Official figures obtained by The Herald show 10 of Scotland's 18 higher education institutions saw numbers from England, Wales and Northern Ireland drop in 2012/13 - when fees were charged for the first time.
The decline is important because the Scottish Government's decision to stop funding such students and allow universities to charge them fees was intended to open up a new stream of income for the sector.
Instead, it appears many universities lost out as students from the rest of the UK (rUK) turned their backs on Scotland.
Institutions that saw a decline included Abertay, Dundee, Edinburgh Napier, Glasgow, Queen Margaret, the Royal Conservatoire, Strathclyde and University of the Highlands and Islands.
Overall, numbers of rUK students coming to Scotland increased by 5% between 2011/12 and 2012/13 - from 5390 to 5650 - but the rise was concentrated in a handful of universities.
The biggest winner, according to figures from the Higher Education Statistics Agency, was Edinburgh, with a number rising 40% from 1215 to 1710. St Andrews also did well, with an 8% hike in rUK students from 580 to 625.
Estimates suggest the first year of fees alone will net Edinburgh some £15 million, although the institution would have been paid a lower fee by the Scottish Government for some of these students under the previous system.
Gordon Maloney, president of NUS Scotland, said: "These figures show that many institutions should have been careful what they wished for in advocating £9000 fees.
"When higher fees for rUK students were first brought in we warned about the dangers of creating a market in education in Scotland and these figures provide compelling evidence that we were right to oppose it because many universities are not benefitting."
Mary Senior, Scotland official for the UCU academic and support staff union, said fees were discouraging poorer students from applying.
She said: "We worry that the more expensive degrees on offer in Scotland to students in the rest of the UK means that only people prepared to take on larger debts will study here."
Alastair Sim, director of Universities Scotland, said: "At a sector level the policy seems to be effective, with Scottish universities still in demand from the rest of the UK and places for Scots are protected. However, we're still in the midst of flux and the UK Government's recent announcement to uncap the number of university places available in England will inevitably have implications for Scotland."
A spokesman for Edinburgh University said: "We are focused on attracting well-qualified students from all backgrounds and work hard throughout the UK to generate student admissions.
"Edinburgh also offers the most generous bursary package within the UK for those on the lowest household incomes, making study an affordable reality."
A spokesman for Glasgow said: "Numbers of applicants and those admitted can fluctuate, and it is impossible to cite with complete certainty what caused the slight dip. We continue to see high demand and are confident Glasgow will continue to be a university of choice for significant numbers of students from both Scotland and elsewhere."
The money Scottish universities make from rUK students is increasingly important, with institutions here set to make an annual income from this source of at least £140m by 2015/16.
Fees of up to £9000 a year were introduced by Scots universities for rUK students in 2012/13 as a result of policy changes in Westminster, which could have led to institutions here being seen as a cheap alternative.
A spokesman for the Scottish Government said: "Scotland was the only country in the UK to see an increase in university entrants in 2012/13, in contrast to significant decreases elsewhere.
"These figures show that the sector has not only remained resilient in the face of pressures but attainment and the international reputation of one of the world's most respected higher education systems remains of a very high standard."