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Emeritus Prof Khyla Russell, of Karitane, sits on the Ngai Tahu Research Consultation Committee and is on the runanga for the coastal East Otago Taiapure fishery, established by the local hapu.
Despite what she described as a decade-long relationship between the department and the Taiapure, Prof Russell said she only became aware of the proposal to get rid of three academic jobs earlier this week.
Another member who worked at the university raised it at a meeting, she said.
"I have to say we were more than a little bit shocked. It is really, really bad. It's not like they're miles away.
"We've established really good friendships and research collaborations."
She questioned whether the university was keeping to its memorandum of understanding with Ngai Tahu.
A university spokeswoman said the university had an obligation to consult with the iwi at governance level, which "does not extend to operational matters".
"This is an employment matter between the university and its staff. However, staff have sought iwi input, and we welcome their feedback."
Prof Russell described the department as one of the greatest contributors of research to the Taiapure and the freshwater mataitai system on the Waikouaiti River.
Contributions marine scientists and students had made included building on the understanding the iwi already had of the coast, and providing scientific explanations for phenomena such as changes in the size of shellfish or changes in abundance of stock.
The knowledge enabled resources to be better managed, and the Taiapure had built strong relationships with "amazing" undergraduate students, some of whom Ngai Tahu had gone on to employ at doctoral level.
"How can you examine all the things that are in the ocean if you shrink a department of brilliant or potentially brilliant future scientists ... it makes absolutely no sense whatsoever. I find it very disconcerting," Prof Russell said.
A public consultation on the proposal, which would involve the review of eight full-time academic jobs and the loss of three - as well as operational changes including the sale of two boats, and some potential changes to professional positions - is running from October 4 to 25.
Prof Russell "lived in hope" she would get the chance to sit down with the university and talk about the proposal.
She was making a submission, and said others would be prepared by the runanga and community.