La Trobe University is concerned about a potential negative impact on student enrolments following the federal government's tertiary reforms.
The reforms announced by federal education minister Dan Tehan on Friday included a shake-up of university fees.
The cost of law and commerce courses will increase by 28 per cent while the humanities courses will cost 113 per cent more.
Students taking on teaching, nursing, clinical psychology, English and languages will pay 46 per cent less, agriculture and maths students will pay 62 per cent less for their degree and people studying science, health, architecture, environmental science, IT, and engineering will have a decreased course cost of 20 per cent less.
Other changes included in the reforms included the possibility of increase the number of university places by 39,000 over the next three years and to 100,000 more by 2030.
La Trobe University said in a statement it was worried the fee changes would affect the enrolments of low socio-economic, Indigenous and regional students wanting to study humanities, law and business disciplines.
"Shifting the burden of undertaking study in these important disciplines to students may ultimately be counterproductive to developing the skills Australia will need for future jobs and economic activity," the statement read. "We broadly welcome the addition of new places for domestic students, noting that we will need to understand and review the details of the proposal before we can give definitive responses about how this will impact La Trobe."
At his National Press Club address, Mr Tehan said 60 per cent of students will see a reduction or no change in their student contribution.
"We will also incentivise students to make more job-relevant choices, that lead to more job-ready graduates," he said.
"To deliver cheaper degrees in areas of expected employment growth, students who choose to study more popular degrees will make a higher contribution."
The La Trobe University statement said there was value in incentivising students to take on courses aligned with areas of expected employment growth.
"This includes areas for which La Trobe is already recognised including education, nursing, STEM, IT and agriculture," the statement said. "However, we also place high value on humanities, law and business subjects and a multidisciplinary approach to areas such as STEM, health and education.
"This is why... we have created multi-disciplinary degrees such as the Bachelor of Humanities, Innovation and Technology."
Bendigo MP Lisa Chesters said she was still working through the details but concerned for students who would be paying more for tertiary education.
"After hearing the minister speak this morning, I was disappointed for our younger people," she said. "Fees and the cost of a degree are already a barrier of going to university and increasing (fees) means more people won't go to university."
Ms Chesters said students arts or humanities subjects are important to some careers.
"A young person might want to think of studying ancient history and study nursing (instead)," she said. "The students I met studying history are studying to be teachers. we should want history teachers to understand history.
"People studying humanities are looking careers in advocacy and policy areas. We want people to have research analytical skills for that, so it was disappointing to (fees increased) rather than funding a sector properly.
"If (the plan is) are to lower fees for course nursing and engineering, I welcome that."
Regional universities are also expected to benefit from an additional $400 million over four years for regional students, universities and communities to lift higher education attainment.
Reforms will also establish the Regional Education Commissioner and offer a $48.4 million research grants program to fund regional universities to partner with industry.