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Oceans and Fisheries Minister David Parker acknowledged the most recent changes, set for October, included high valued shared fisheries.
Among the changes for the South were a decrease for school shark, as indicators pointed to a potential sustainability risk with overfishing likely occurring.
Therefore, the Southland and sub-Antarctic catch limit would be lowered.
"All submissions received during consultation were in favour of decreasing catch limits to ensure sustainability of this stock, however, submitters and respondents varied in terms of how much these limits should be reduced. I wish to acknowledge the responsible position taken by industry in its submissions," Mr Parker said.
Consultation submissions released last week included one from the Fiordland Marine Guardians, the governance group of its area.
The group supported the option to decrease the catch allowance by about 30%.
"The goal to rebuild the fishery aligns with the Guardians’ vision for the Fiordland Marine Area," the group said.
While the Riverton Fishermen's Company agreed the reduction was best, its submission explains it thought the 30% was a bit overboard, and instead suggested 20% to 25%.
The crew of its school shark boat had been telling them for several years it had been getting harder to catch, and it was harder work for less shark.
Nicholas White submitted on behalf of Jacob Fishing Ltd and N & H White, and shared that same concern.
"We have been fishing this stock for 28 years. In the last 20 years we have had to increase our fishing effort almost annually to catch the same amount of fish — therefore noting what we presume to be a gradual decline of this fish stock."
Galeos Fishing Company Ltd director Bevan Murcott was concerned for the fishery, but would rather see the whole fishery have a reduced catch limit.
Other changes included a blue cod decrease in Otago, an increase in southern bluefin tuna everywhere, an increase for gemfish from the South Island east coast down, and ling in Southland, and a decrease in hoki catch limits across the country.