The proposal was part of a national restructuring plan aimed to cut the ministry's planned staff numbers by 29 full-time equivalent jobs - mostly by centralising fisheries management positions in Wellington and Auckland.
That included reducing Dunedin's fisheries management staff from 18.3 to 10.8 full-time equivalent staff.
Yesterday afternoon, chief executive Wayne McNee told staff of the outcome of consultation on the proposal, which included a decision to reduce Dunedin jobs by 4.5 full-time equivalent staff to 13.8.
Public Service Association assistant national secretary Jeff Osborne said the Dunedin-based fishery managers oversaw fishing for Bluff oysters, 92% of the blue cod quota for New Zealand and 71% of the country's paua quota.
Inshore fishery management jobs were also due to be cut in Nelson (7), Napier (2) and Auckland (6).
Mr McNee said the reduction in job cuts for Dunedin was the result of submissions from staff which justified the retention of fisheries management staff in the city.
The jobs retained were a fisheries management team leader and two analysts.
Fisheries management staff in the Dunedin office would now be required to apply for the remaining positions and would have the option of applying for five project management roles that could be based in any of the centres facing cuts, he said.
Five similar positions would be based in Wellington, and Dunedin staff could apply.
The new structure would become operative on October 1.
Mr Osborne said: "This is highly specialised work that requires a great deal of local knowledge."
The cuts made a mockery of the Government's claim it was moving public service workers on to the front line, he said.
