Deakin Vice-Chancellor Professor Iain Martin announced an organisational change to all staff this week that could see about 1000 workers either face some shift in their role or have to reapply for their job.

Professor Martin in a statement said the proposed changes were "necessary to secure Deakin's financial future" while ensuring services were effective.

"There is no doubt that this is an incredibly challenging time for both Deakin and the wider university sector in Australia," he said.

The Standard understands that job losses at the Warrnambool campus could involve less than five positions, although no final decisions have been made.

It comes after the university last year cut six positions at the campus, mostly in administration, during a restructure due to the coronavirus pandemic. Deakin cut about 300 jobs across all campuses last year.

Warrnambool campus National Tertiary Education Union academic vice president Michael Callaghan said it was disappointing another round of cuts would occur.

"Rather than the university protecting their greatest asset - their employees - by going into debt, they are throwing those people on the scrap heap," Dr Callaghan said.

But he said while the total number of jobs to go was high, the campus would be affected "proportionally" to its size.

"The Warrnambool campus is incredibly efficient as it stands because of the history of what has happened," Dr Callaghan said.

"While there will be jobs under pressure, that pressure is going to be far greater in areas of the university where there is a greater depth of staff."

But Dr Callaghan said it was unsettling for staff to have to reapply for their positions, particularly given the stress of wider health restrictions during the past 18 months.

"Everybody has a sword over their head," he said.

"The main concern I and the union have is the protracted time individuals have been exposed to high degrees of stress over this period coupled with working from home."

Asked about the stress on staff, a university spokesman pointed to a series of services such as counselling and coaching to help employees during the change.

The workplace change will take a minimum of four weeks for parties including the NTEU to reach agreement on.

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