The Ministry for Primary Industries has been "captured" by the fishing industry and is failing in its duty as regulator, Greenpeace says.
A leaked internal government report shows serious under-reporting of fish in the southern blue whiting fishery, the environmental organisation says.
The report, produced by the Ministry of Primary Industries and released by Greenpeace, showed a similar pattern of under-reporting and dumping of fish to that in the hoki industry, the environmental organisation said.
Last week Greenpeace released a 2012 report about the hoki fishery.
Greenpeace executive director Russel Norman said compliance officers found lots of evidence and pushed for prosecutions.
But he said the ministry believed prosecution would have no long-lasting effects and that it saw problems from the fishing companies' perspective.
Greenpeace has called for an independent public inquiry into the fisheries management system and its regulator.
However, the ministry said its procedures have changed since the 2012 report.
It said the report was never meant to be evidential.
Executive director Russel Norman said the practises would continue to be widespread until the government forced the ministry to enforce the law.
He told Morning Report the fishing industry and MPI wanted a MPI-led review.
"From the point of view of the public we need an independent inquiry.
"Whether it's commission, whether it's a royal commission, it has to be under the Inquiries Act which has the powers to call witnesses, take evidence in secret - a lot of people are scared to tell the truth - so that they can actually find out why the regulator is failing to enforce the rules on this repeated, systematic, illegal behaviour of which they themselves have discovered."
However, the ministry said the 2013 report pre-dated work that had been done to improve reporting the southern blue whiting catch.
In the report, MPI investigators said a "conservative" estimate was that dumped fish amounted to between three and six percent of the total allowable catch - up to 2677 tonnes.
Conservation advocacy group Forest and Bird said neither MPI nor the fishing industry appeared to have shared the southern blue whiting report with the Marine Stewardship Council.
"During the period the offending was taking place, the ... fishery was under assessment by the MSC, subsequently certified as sustainable in 2012, and sold around the world on that basis," Forest and Bird said in a release.
The government is currently considering scrapping the roll-out of cameras on-board fishing vessels.
The former National government came up with the plan last year, saying it would protect the sustainability of fish stocks and act as a deterrent against illegal activity.
But new fisheries minister Stuart Nash said in February that National had forced the plan upon the sector, and he was getting advice from officials on what should be done.
Forest and Bird chief executive Kevin Hague said the latest leaked report showed cameras on boats "can't come soon enough".
"Sadly, the fishing industry's worst enemy is themselves. The onus is now on them to prove that they are committed to transparency and truth-telling."
MPI's compliance and investigations manager Gary Orr said the report was to identify the extent to which the reporting of catch may have been inaccurate and the reasons for that.
As a result of that work, the industry changed its processing procedures which resulted in more accurate reporting, and MPI altered conversion factors to ensure the way the fish was processed was more transparent, he said.