Students from the rest of the United Kingdom will pay £6,000 less to do a degree at Abertay University than at Dundee.
Both institutions chose Tuesday to announce the tuition fees they will charge from the start of the 2012-13 term.
Dundee University has opted for the maximum £9,000 a year, with a £27,000 cap. New three-year courses with the same price tag will be developed.
Abertay will also charge for only three years of study, but it has chosen to set a fee of £7,000 a year.
Both universities will use much of the extra income to pay for bursaries for poorer students.
However, student leaders said they were disappointed by the rises, which will apply to students from England, Wales and Northern Ireland, but not to those from Scotland or from other European Union countries.
Professor Nicholas Terry, acting principal at Abertay, said: “While historically we have recruited fewer students from the rest of the UK than other Scottish universities, we have seen a noticeable increase in recent years, particularly on to courses such as computer games technology and computer arts, where we are an internationally recognised centre of excellence.
“We believe the fee level we have chosen is a realistic and highly competitive rate that will reflect the government’s intention of preserving and enhancing provision for Scottish-domiciled students, while maintaining a healthy flow of cross-border students that have always contributed so much to the richness of the student experience we offer.”
The president of Abertay University Students’ Association, William Mohieddeen, said he appreciated management had refrained from imposing the maximum charge but was still concerned less well-off students would be discouraged from applying.
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He said fee rises were “a black mark on the copybook of Scottish higher education” and he urged ministers to find a long-term solution to university funding.
The first batch of three-year honours programmes at Dundee University will be launched next September and the range on offer will be expanded in future. The university said the programmes will allow students to gain an honours degree in the same length of time as in the rest of the UK, which would significantly reduce the total cost of a degree once living costs were factored in.
Scots students who have passed Advanced Highers or who have already studied at college will be able to embark on these courses too.
Principal Professor Pete Downes said: “We fully appreciate the views of students and their families looking at the costs of attending university. By offering competitively-priced three-year programmes which of course mean a year’s less costs in living expenses such as accommodation and combining this with very high academic standards, we think we have a very attractive offer for students.
“Many of our other courses will continue to be offered on a four-year basis, where we will cap total fee costs at £27,000. However, we are actively working on developing a three-year option for many of these courses.”
A spokesman for Dundee University Students’ Association said: “Although the increase to £9,000 is higher than we would have hoped for, we welcome the commitment of the university to offer significant bursaries to ensure students from the rest of the UK can continue to study at Dundee and are not put off by the costs that this would incur.
“DUSA will be working extremely hard to ensure that the bursaries are made available to those students who need them the most and that the student experience is not damaged by the proposed transition to three-year degrees.”
Janice Aitken, branch president of the University and College Union (UCU), said: “Even with the cap of £27,000 we have serious concerns about the way in which recruitment may be affected by this decision.
“Whilst we acknowledge that Dundee is a less expensive city in which to live and study than some others in the UK, there is still the possibility that less well-off students from the rest of the UK will be put off by the high level of fees and will choose either to study nearer home or miss out on higher education altogether.”