The gap year plans of Aitken College year 12 students Sarah Brown and Kaitlyn Walker, both 17, are in doubt after Tuesday's announcement of changes to university fee structures.

Sarah planned to study science at Melbourne University after taking a year off to travel to Europe. Instead, she may have to settle for a trip in the 2015 midyear break to save money for her course costs.

''Because of fees rising, I just don't think [a gap year is] worth it in the long run,'' she said. ''I may as well start [university] next year to save money.''

On Tuesday the federal government revealed universities would be able to set their own fees from 2016 and apply real interest rates to student debts for the first time.

Experts such as Bruce Chapman, the architect of the HECS student loan scheme, predict university degrees will cost up to three times as much, with some graduates attracting debts of $120,000 or more.

Since budget night it has emerged that 2014 school leavers will escape the new fee regime only for the first year of their university study.

After 2015, and for the remainder of their courses, they will pay whatever fee is set by the university.

Students from this group planning a gap year will have to pay the full charges when they return to start their courses, even if they enrolled in 2015.

The university sector is in a state of confusion over how the new fees will apply to prospective students.

A spokesman for the Department of Education said the government was yet to determine when providers must publish their new fee arrangements.

''Currently, a provider must publish a schedule of fees for all units of study … on or before the earliest enrolment date,'' the spokesman said. ''This gives students to access information about fees before they enrol.''