Federal Education Minister Dan Tehan said on Friday commerce was among "popular" degrees set to cost more, while other degrees linked to labour needs would see fees significantly dropped.

National Tertiary Education Union Warrnambool campus vice president Michael Callaghan said the Warrnambool commerce course was already strained and he urged the government to "re-think" which degrees should cost students more.

"The loss of the majority of key staff in the commerce area has already resulted in a course offering that provides limited choice to students," Dr Callaghan said.

He said most students could do their first year of the course in Warrnambool, before needing to travel to Deakin's Geelong or Melbourne campus to complete the degree.

"There have been a lot of conversations about what might re-invigorate that course, however given the government's move today it's going to make that all the more difficult," Dr Callaghan said.

He said many Warrnambool financial firms were built off the back of a strong accounting major at the university.

"It was the underpinning and delivery of those courses that have led to significant prosperity for the town," Dr Callaghan said.

Steve Harris from Warrnambool financial planning business Silvan Ridge, said he had employees who went through the course and the fee increases were "disappointing".

"Doing their study in this area enriches them and gives us the ability to tap into the talent," he said.

"It's disappointing to see because in our industry in particular it's difficult enough to get people at grass roots level."

Sinclair Wilson human human resources director Mark Robson said at least 30 per cent of the firm's staff graduated from the course.

But he believed the fee increase might make studying commerce in the south-west rather than in Melbourne more attractive to the region's school leavers.

"Studying in a regional centre may outweigh some of the costs," Mr Robson said.

Dr Callaghan said the union believed the government had increased the cost of degrees critical of it, including arts and law.

"Marginalising these specific professional areas indicates a desire by the government to reform higher education such that it no longer provides that critical commentary of government activities," he said.

"Part of your degree is developing knowledge to view the world, critique it and make the ethical and moral decisions in line with your professional obligations.

"My major concern here is that in reducing funding in law and to business, such that becomes the domain of the wealthy, will heavily influence the type of graduate that comes from those courses."

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