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Under a proposal released to staff last Friday, eight full-time academic positions in the department are due to be reviewed and three lost.
Consultation on the proposal is open to the public until October 25. A petition from students calling for staff numbers to be retained has gained more than 2600 signatures.
TEU Dunedin organiser Kris Smith had consulted with staff and said the union's stance was the university should cross-subsidise the department, which has been in deficit each year since 2013.
"TEU members think a responsible fiscal target can be reached without gutting the programme and the people," she said.
"Aotearoa is a maritime nation ... much of our income comes from marine exports.
"Investment in marine science isn't a luxury add-on. It informs who we are and what we do."
The eight "talented" staff members contributed to programmes of national importance and had all received awards.
Their expertise ranged from dolphins and whales to fisheries restoration and large-scale ocean dynamics, climate change impacts on marine life, and coastal oceanography.
"They can't necessarily teach each other's material."
She questioned why no "major cuts to operating expenses" had been proposed despite that component being a major contributor to the deficit, due to be higher than $4.2 million this year.
A response from the university said the bulk of the deficit was due to money spent on staff salaries, and most of the department's expense was carried by other departments.
"If the proposed changes go ahead the university will still be providing a significant subsidy to the department."
Under the proposal, the university has said it could sell two of its fleet of six boats, and one lab position would be transferred to a different department, another position being left vacant for the time being.
Oceanography student Rachel Worthington said the department should not be viewed solely through the lens of cost.
"We are so much more than just our financial statements. This affects so many more people than just the staff and students of the department," she said.
"The university, just a few weeks ago, sent a senior leadership member to the Strike for Climate Change and promised that the university was going to take a strong stance in support of climate change action.
"It seems to me that they aren't committed to protecting our world-renowned climate change researchers."