Officials are sceptical of a study that claimed more than half of the fish caught in New Zealand waters do not show up in official records, Prime Minister John Key says.
Opposition parties say urgent action is needed to protect fisheries, after the study recommended that the quota management system undergo "robust critical review".
Labour wants an independent review into the quota management system, and the Green Party says more government observers are needed on ships.
The total catch between 1950 and 2010 was 38.1 million tonnes, the new study says, compared with a reported catch of 14 million tonnes.
The main reasons for this difference were unreported commercial catch and fish which were discarded because they were too small, uneconomic, or because the fisher had no quota.
Lead researcher Glenn Simmons, from the New Zealand Asia Institute at the University of Auckland Business School, said the quota management system had inadvertently rewarded misreporting and dumping.
The paper quotes an MPI investigation in 2013, which said: "The sight of large, perfectly good fish being systematically discarded in such large quantities could have a huge negative effect, as it could easily stir up an emotive backlash from not only the New Zealand public, but from international quarters as well".
It added: "This combined with the fact that we have known about these dumpings/discarding issues for many years, and would appear to have done little to combat it, would be very difficult to explain and be unpleasant at best."
Asked about the findings, Mr Key said earlier research by Niwa had estimated the discarded catch rate at about 6 per cent.
"For a considerable time now - but I accept, increasing in recent times - we have had observers on boats, we have had cameras on boats, we have had GPS tracking."
MPI's director fisheries management, Dave Turner, said its initial review of the report has raised concerns about methodology and conclusions.
"The report simply can't draw adequate conclusions about sustainability, as its authors attempt to, because the measure of sustainability is abundance - that is, the amount of fish in the sea - not extraction as the report attempts to analyse.
"We have decades of peer-reviewed science that shows steadily increasing levels of abundance. The situation now is that New Zealand fisheries are healthy overall."
Seafood New Zealand chief executive Tim Pankhurst attacked the report as lacking scientific credibility and using a "hopelessly biased" sample.
"New Zealand's fisheries management is recognised as one of the best with one of the highest compliance levels in the world."
• New Zealand's reconstructed marine catch totalled 38.1 million tonnes between 1950 and 2010, which is 2.7 times the 14 million tonnes reported to the United Nations' Food and Agriculture Organisation (FAO)
• Since the Quota Management System (QMS) was introduced in 1986, the total catch is conservatively estimated to be 2.1 times that reported to the FAO
• Unreported commercial catch and discards account for the vast majority of the discrepancy
• Recreational and customary catch was 0.51 million tonnes, or 1.3 per cent
• Only an estimated 42.5 per cent of industrial catch by New Zealand flagged vessels was reported
• 42 per cent of the industrial catch was caught by foreign-flagged vessels, which dominated the catching of hoki, squid, jack mackerels, barracoota and southern blue whiting -- some of the most misreported and discarded species.