University top-up fees could further undermine courses struggling to recruit students, government research warns.
There are fears for some science and technology courses
Universities fear that some technology, science and language degrees, which take four years to complete, will prove less popular because of the extra cost.
And it is feared English universities will "cream off" the brightest Scottish students with generous bursaries.
The Institute of Education research also suggests part-time students, not eligible for bursaries, may lose out.
The IoE questioned representatives from 15 institutions in England about the new student funding arrangements, as well as six Scottish institutions to assess the expected impact of the changes on them.
The research - which was commissioned by England's Department for Education and Skills - is the first stage in a two-part study which will report again after variable fees (commonly known as top-up fees) are introduced.
The findings, at this stage, show institutions are uncertain about the impact the new arrangements will have on the recruitment of undergraduates.
Currently students in England pay tuition fees of £1,175 a year, but - from September - they can be charged up to £3,000 a year, though many universities are offering a range of bursaries to assist.
Fees will no longer have to be paid in advance, being covered instead by an official loan repayable after graduation.
Scottish students have always had their fees paid for them and, after they graduate, have to pay an endowment "in recognition of the higher education benefits they have received".
The IoE study raises particular concerns about the impact of the new funding arrangements for four-year degree courses, such as languages and the Bachelor of Education degree.
And the report highlights that some courses, already struggling to recruit undergraduates, could fare even worse under the new system.
Most of the new universities surveyed believed the changes would "cause them to become more strongly regional in their recruitment".
It was felt this could lead to strained relationships with competitors in the region and the "erosion of collaboration between institutions".
And there is concern that English institutions will, through bursaries, "cream off bright Scottish students from disadvantaged backgrounds".
"Also, the competition among the English institutions has led them to improve teaching and social facilities - what students see during recruitment - while the Scottish institutions have not needed to and so may look dowdy by comparison," the report says.
The research found students generally felt the benefits of higher education outweighed fears of debt.
It found evidence that they would gain directly through improved teaching and facilities.
"There was a widespread sense of needing to respond more quickly and positively to student requests, prior to and after admission," the report says.
But there might also be "heightened expectations of service".
"There was concern in some institutions that students would have unrealistic ideas about what their fees would be 'buying', and this might lead to some difficult tensions between students and academic and administrative staff."
A spokesman for the Department for Education and Skills said: "As this report itself makes clear, higher education institutions can only guess what impact students fees will have.
"Elements of this research necessarily include speculation about future outcomes. What we do know is that we are bringing in a fairer system essential to maintain a world-class higher education system," he said.
"Crucially from next September, students don't pay a penny for fees or loans until they are in work and earning more than £15,000."