Commercial fishers could get government compensation of about $20 million if changes to the Marine Reserves Act go ahead, Environment Minister Nick says.
The Government is proposing to update the 45-year old legislation, creating recreational fishing parks, marine and seabed reserves and sanctuaries in the Hauraki Gulf and Marlborough Sounds.
The new Marine Protected Areas Act would allow some commercial fishing in the Hauraki Gulf, but impose restrictions in the inner gulf on popular species like snapper, John Dory and kahawai.
The 80 commercial vessels currently operating in the proposed park area would otherwise be allowed to continue fishing, with a focus on prolific breeding species such as flatfish.
One of the country's largest fishing companies, Sanford, questioned the impact of the proposals on fishing quotas.
Chief operations officer Greg Johansson was concerned the proposals could undermine the system.
"If people are going to have, forcibly removed, their rights to catch fish, that's potentially going to change the way they behave in regards to their stewardship of the resource.
"The document's unclear as to whether this is a willing-buyer, willing-seller transaction or this is a confiscation of existing property rights, and if that's the case then I think all New Zealanders should be very concerned."
But Dr Smith told Summer Report the existing Marine Reserves Act allowed reserves to be created without any compensation.
"What these proposals do is ensure there's a greater involvement of both recreational and commercial fishers where those sorts of marine reserves are created.
"Where you are wanting to effectively take a resource currently used by the commercial fishers in Hauraki and Marlborough sounds ... what we're saying in these areas is that we would pay fair compensation."
The commercial fishing industry took about 1000 tonnes annually from the Hauraki Gulf and Marlborough Sounds areas out of a total 600,000 tonne catch, Dr Smith said.
The New Zealand Fishing Industry Guild said smaller commercial operators would be most affected and the protection boundary could force them to work further out to sea.
"Some of them will go further out because they want to stay in business, which then potentially puts them at risk because they're smaller boats that could be fishing in a more dangerous [area]," said guild executive secretary Ian Mathieson.
"It also puts more pressure on the existing boats in that area, which will be more the trawler fleet," he said.
Mr Mathieson said the government plans "changed the game a little bit."
"The quota management system has been around for a long time, and it does provide these rights in perpetuity.
"The government's proposal is a departure from that in extinguishing quota rights which were given to, I guess, commercial fishermen and iwi as part of Treaty settlements."
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Commercial fisherman Michael Bradley breeds and fishes for flatfish in the Marlborough Sounds but said that under the proposed changes he would have to stop.
Mr Bradley said local Maori families, such as his own, had been fishing in the Sounds for more than 800 years and a one-off compensation cheque isn't good enough. He said he would take High Court action.
Proposals fail to please recreational fishers
Keith Ingram from the Recreational Fishing Council said the plans were a step in the right direction, but fell short of earlier suggestions that the whole Gulf would be a recreational fishing park.
"This is significantly short of that. It doesn't and won't impact on the fishing activities of the industrialised fishing methods of trawling and Danish seining."
Environmental groups Forest and Bird and WWF New Zealand asked why the protection area did not extend outwards to include the Exclusive Economic Zone (EEZ), 200 nautical miles offshore, rather than the 12-mile limit of the country's Territorial Sea.
Mr Ingram said fish that were too small for recreational fishers to keep would simply be caught by commercial fishers nearby.
"Fish conserved by the recreational sector ... they'll just go back out into the waters where the commercial fishermen can catch them."
Dr Smith said it was not in recreational fishers' interests to ban all commercial take, such as with a species like kina which eats sea grass.
"If you banned the commercial taking of kina in the Hauraki Gulf, that would allow the sea grass numbers to decline, which would adversely affect the recreational snapper fishery because that is where the snapper breed."
He said popular inshore fish offered more value on the end of a child or a tourist's line, in a broader sense for New Zealand, than being caught in a big net.
Submissions on the proposals can be made until 11 March, and will then be considered before a draft bill is drawn up.