The Ministry for Primary Industries (MPI) has announced a new independent review into previous operations investigating the illegal dumping of fish.
It comes after leaked reports raised fresh questions around the potential scale of the problem - and how MPI has responded to it.
MPI director general Martyn Dunne said there had been "much comment" this week around an MPI compliance investigation, dubbed Operation Achilles, into potentially illegal discarding of fish by some South Island-based fishing vessels in 2012 and early 2013.
Yesterday, NewsHub reported one of two leaked reports, focused on Operation Achilles and written by an MPI investigator, estimated that 20 to 100 per cent of some quota fish were being dumped each time the net came on four of the five vessels monitored.
The Green Party responded by claiming MPI was "looking the other way" and called on the Government to overhaul the quota management system that regulates the industry.
In a statement released today, Mr Dunne said he had launched an independent review into the circumstances around Operation Achilles - including the decision not to prosecute individuals associated with the potentially illegal discarding.
"I place a high priority on the ministry having strong credibility with the public when it comes to our role as the regulator of fisheries in New Zealand and our role in holding people to account when illegal activity takes place."
The review would also consider matters relating to a report of a second investigation known as Operation Hippocamp.
"This investigation also examined matters in relation to potentially illegal fish discarding."
An independent Queen's Counsel would be engaged to undertake the review, with terms of reference still to be finalised.
Rino Tirikatene, Labour's spokesman for fisheries, said a wider inquiry was needed.
"MPI is in crisis mode at the moment. The fact that they were denying these reports just yesterday, and now today they have changed their tune...it just shows that they are in disarray and they are desperate.
"Let's hope that this inquiry is not just an inside coverup job."
The concerns raised by the leaked reports came just two days after an Auckland University study explosively claimed New Zealand's actual fishery catch was 2.7 times more than what was reported.
Its methodology and conclusions were quickly challenged by MPI and the seafood industry.