Figures show that applications to study at Welsh universities this September have increased while those received by English institutions have fallen.
UCAS say 13,000 fewer students have applied for courses this year
Statistics from admissions service Ucas show formal inquries to colleges in Wales have risen by 0.5%.
There is also a rise of 1.6% in Scotland but in England applications have fallen by 3.4%.
National Union of Students (NUS) Wales said top-up fees in England and fear of debt could be to blame.
This year students who want a place on undergraduate, some postgraduate courses in England will have to pay top-up fees of up to £3,000 a year.
In Wales, fees for all students will remain at £1,175 for another year.
NUS Wales president Dylan Williams said: "These figures show that the fear of debt is a major concern for students who are looking at where to study next year.
"I don't think it is any co-incidence that in England, where top-up fees are going to be charged for the first time, there has been a drop in the number of students applying, while in Wales and Scotland, where there will not be top-up fees, applications have risen.
"It is worrying that the country could be missing out on thousands of doctors, dentists, teachers and engineers because the fear of debt has put them off applying to university."
Students expecting to study this September had to make their applications by 15 January.
Almost 13,000 fewer students have applied for courses in England compared with last year, but the numbers applying to Welsh colleges have risen by 292.
The University of Wales, Newport, said applications for its courses had risen by more than 12.1% and Swansea University confirmed its figures had gone up 9.5%.
Welsh universities will be able to charge top-up fees of up to £3,000 from 2007, as in England.
But students who normally live in Wales and studying in Wales will be exempt - having to pay only £1,175, with the rest being paid by the Welsh Assembly Government.
The assembly government said the deal agreed by the assembly in June did not apply to those studying a subject in England not taught in Wales such as veterinary science, but it was looking at the matter.