The Ministry for Primary Industries (MPI) is under fire over a leaked report on illegal fishing practices in our deepwater hoki fishery.
The Government report shows some of the biggest commercial fish companies are unlawfully dumping and under-reporting thousands of tonnes of fish.
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Executive Director Dr Russel Norman says: "People should be very concerned both for the environment, the oceans, but also economically in terms of the future of the fisheries."
Companies singled out in the 2012 Ministry of Fisheries report include McDonald's supplier Talleys, which is accused of underreporting as much as 780 tonnes of hoki in a season.
Sanford was also accused of under-reporting and of compromising a fisheries inspection by removing a computer that had daily catch and processing records.
Dr Norman says the report provides damning evidence against MPI, who are the regulators of the industry.
"It's very clear that the fishery is not being managed properly and it's not being regulated properly," he said.
Dr Norman says it's "profoundly at odds" with public information about fishing industry practices released by MPI.
"Far more fish were being caught than were being reported under New Zealand's Quota Management System, resulting in millions of dollars in savings for fishing companies as they didn't need to purchase quota for the disappeared fish. It also meant that no-one really knew how much fish was being taken," Dr Norman said.
The report said that discarding is of particular concern in the hoki industry as "fishers may increase their economic return by deliberately discarding small, damaged or less valuable fish", therefore avoiding having to pay for the catch as part of their annual entitlement.
Misreporting involves companies recording incorrect weights, quantities, species or landed states to minimise their expenses in relation to their annual catch entitlement.
Deepwater Group chief executive George Clement said in a statement: "Industry fully supports and encourages MPI to routinely undertake assessments of compliance onboard our deep water fishing vessels and to advise industry where performance improvements might be required.
"To the best of our knowledge, no prosecutions were taken in the aftermath of this assessment however MPI did discuss their key findings with vessel operators in 2012 and remedial actions were set in place in response, prior to the 2012 hoki season."
Mr Clement said the industry "supports MPI compliance taking the necessary actions, including prosecution as and where applicable, where operations are clearly non-compliant and there is evidence to support this".
Talleys has been contacted for comment.
MPI's acting director of compliance operations Gary Orr has defended the fact that the report did not lead to prosecutions, saying it was analytical and not of a standard to be used as evidence in court.
"If we're trying to achieve long term compliance it's been proven in the past that prosecution is not always the best option for doing that. It will impact on a short term, but long term no, so we need to have more effective ways of changing behaviours."
Mr Orr said MPI has "far greater confidence" in the hoki fishery than it did at the time of the report and it does not reflect the current state of the fisheries.