Fees are expected to more than double for environmental studies and communications students when they are deregulated in 2016, while mathematics students are set to emerge as winners.
The federal Department of Education this week released new funding rates for students who enter university from 2016, with total government funding declining by 20 per cent.
Universities will be able to charge as much as they want on top, with graduates to pay back the debt once they start earning $50,638.
Government funding for environmental studies students will fall by 44.5 per cent, according to an analysis by Grattan Institute higher education program director Andrew Norton. This means universities will have to charge students $9662 more a year to maintain current funding levels – a 112 per cent increase.
Commonwealth support for communications students will drop by 50 per cent, meaning budding journalists and public relations professionals would pay $6010 more a year – a 99 per cent increase. Fees for engineering and science students would rise by at least $5059 a year, a 58.7 per cent increase.
Nursing and teaching students face fee increases of at least 19 per cent and 23 per cent respectively.
Fees would rise by 49 per cent for visual and performing arts students, by 43 per cent for social studies students and by 42 per cent for agriculture students.
Mr Norton said these were the minimum increases he would expect and fee deregulation would allow highly regarded universities to charge far more for popular courses.
Education economist Bruce Chapman, the architect of the HECS repayment scheme, predicted fees would triple at top universities.
Education Minister Christopher Pyne said on Thursday he expected fees for some courses to rise and others to fall.
While the government is cutting support for most disciplines, mathematics and statistics students will receive a 23 per cent funding increase. Fees for a mathematics degree would fall by 26.3 per cent at current degree costs.
Commonwealth funding for humanities will rise by 8.9 per cent while support for allied health and clinical psychology will remain stable.
Minimum student contributions for law, accounting and commerce are expected to remain stable.
By Matthew Knott