The number of fish caught in New Zealand waters has been under-reported for six decades, with the true catch nearly three times official figures, according to a new report.
The study - conducted by the Fisheries Centre at British Columbia University, in collaboration with Oxford and Auckland universities - also exposes deliberate and systematic fish dumping, institutionally embedded misreporting and high levels of wastage.
The report also includes references to two ministry investigations in which the ministry said it had strong evidence of serious offending that could be a PR disaster, if released publicly.
One of the lead researchers, Auckland University's Glenn Simmons, told Nine to Noon misreporting has long been seen as a problem with fishermen.
But he said the introduction of the quota management system in 1986 created incentives to misreport once the fish were brought back on land.
"As one interviewee explained to me, for a while, fish for cash was the biggest thing in Auckland."
Greenpeace said the ministry wasn't fit to monitor the country's fishing stocks and its independence had been thrown into question.
Its executive director, Russel Norman, said it was incredible the regulator wasn't interested in cracking down on offending, and appeared more concerned with keeping it secret.
"If you have a regulator, who has evidence in front of them of serious offending, the appropriate response is to prosecute those who are doing the serious offending."
But the Ministry for Primary Industries (MPI) has said there is no cover up and it doesn't release reports into criminal investigations.
MPI director of fisheries management Dave Turner questioned the study's figures, saying Niwa recently reviewed the last five years' catch for six key deepwater fisheries.
"They found that around 95.9 percent was retained and around 4.1 percent was discarded, so yes I agree that there is discarding and misreporting happening, I just disagree with the total sum that this report has come to."
Mr Turner said the ministry was boosting its monitoring and planned to put cameras on all fishing boats in the next few years.
Minister for Primary Industries Nathan Guy told John Campbell he had real concerns about the report.
He said critical comments made by his officials about fish stocks do not reflect widespread problems in the industry and noted that the report goes back to the 1950s, before the current regulations.
"The EEZ wasn't in place until 1977, the quota management came in 1986, the Fisheries Act came in in 1996.
"And yes, from time to time there is misreporting, and yes from time to time there is dumping. With evidence, we take a hardline, we get the evidence together and we prosecute."
Mr Guy said the ministry spends $22 million a year in independent science, often carried out by Niwa, which estimates the discard rate is 6 percent.
He said he would much prefer to believe Niwa than the report, which states the discard rate is 50 percent.