The bill is expected to more than double the cost humanities degrees, and increase the cost of law and commerce courses.

Courses deemed "job-ready" such as nursing and engineering are expected to drop in cost.

Read more: University reform last pass parliament

A La Trobe spokesperson said the university supported many parts of the higher education reform, including regional delivery and an increase in Commonwealth supported places.

But the spokesperson said La Trobe remained concerned about the practical impact of funding arrangements for disciplines such as humanities and law.

Bendigo's Federal MP Lisa Chesters said the funding cut would hurt La Trobe by cutting billions of dollars from higher education.

Ms Chesters said it meant the already struggling sector would have to cut even more jobs to make the difference.

She said La Trobe would be under pressure to change its offering, to make sure they were offering the courses people wanted to study next years.

Ms Chesters said the changes would deny people the opportunity to to study at university.

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She said those who were the first in their family to study at university were particularly likely to be put off higher education by price increases.

"Regardless to your capacity to pay, everyone should have access to a university education if that's the past they choose to go," Ms Chesters said.

"It's critical for our post-COVID recession recovery that we have graduates ready to work in various fields."

The La Trobe spokesperson said the university also welcomed greater flexibility to allocate commonwealth funding to sub-bachelor and postgraduate courses.

The COVID-19 crisis has already put strain on Australia's university sector, taking away its market of overseas students.

La Trobe University has already initiated a voluntary redundancy program in response to the COVID-19 crisis.

By August 239 staff members - including 25 Bendigo workers - had taken voluntary redundancies.

That month it announced another round of voluntary redundancies.

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