Top-up fees will deter students from applying to four-year undergraduate degree courses in science, languages and engineering, a Government-commissioned study has warned.
Students will shun the subjects, which already suffer from a shortage of graduates, to avoid carrying the burden of an extra year of debt, according to the researchers.
Academics at the Institute of Education interviewed staff at 15 higher education institutions last summer for the study, which was conducted for the Department for Education and Skills.
One of the authors of the report, John Farrant, who is a partner at Universitas Higher Education Consultants, said: "Students will emerge with a larger debt if they stay at university for a fourth year. "If it appears that the high fees are a deterrent, then it is likely the universities will offer more generous scholarships or that there will be more of a difference between the bursaries of different subjects."
The report found staff were concerned that tuition fees of £3,000 a year would make recruitment more difficult for science and technology courses.
It says: "A particular concern was over four-year degrees, in science, technology and the year abroad for languages."
The study also found that universities were "uncertain" about what impact top-up fees would have.
But post-92 universities believed more students would be likely to study locally and Scottish universities feared losing students to English institutions that offered more generous bursaries.
The study, which was co-written by Mike Shattock and Paul Temple from the Institute of Education, concludes that Scottish universities may suffer from the introduction of fees.
The report says: "Competition amongst the English institutions has led them to improve teaching and social facilities - what students see during recruitment - while Scottish institutions have not needed to and so may look dowdy by comparison."
The report also argues that increasing fees could "kill" part-time study for courses that do not result in a degree, such as supplementary language classes.