Some of the country's biggest fishing companies have been under-reporting their hoki catch by hundreds of tonnes, according to a leaked fisheries report.
The report has been kept secret from the public for seven years and environmentalists say it casts doubt on industry claims that lucrative hoki is being fished sustainably.
The companies include Sanford and Talley's.
Hoki is the most valuable export fish, earning the country $230 million last year and famously used in McDonald's filet-o-fish burgers.
The Ministry of Fisheries 2011 report said McDonald's supplier Talley's failed to report an estimated 780 tonnes of hoki in one season.
Greenpeace director Russel Norman said such failures meant authorities were not able to accurately set quota levels and the entire hoki stock was at risk of being over-fished.
"It is one of the first big white fish fisheries in the world to get Marine Stewardship Council certification and New Zealand goes around telling the world what a great fishery this is but the truth, as has been revealed by the government's own secret investigation, is that it's anything but."
The report revealed one observer on board a Sanford vessel said the captain gave misleading information about the species they were targeting.
This was so they could fish in an area that was home to juvenile hoki that needed protecting in order to build up future stocks.
Mr Norman said this showed a complete disregard for the health of the fishery.
"It's a concentration of hoki which has up to 40 percent juvenile hoki but there is also adult hoki in there that they actually want to catch so they target this area in order to get this adult hoki, they pull in all of the hoki, they dump the little ones because they only want the big ones."
The report showed under-sized fish or those the boats did not have quota for were hidden by being ground in to fish meal for fish and poultry farms.
It said up to 2000 tonnes of fish was disposed of in this way in a single season.
World Wildlife Fund spokesperson Peter Hardstaff wanted to know why the Ministry had not made the report public and if the recommendation for a further investigation had actually been followed through.
"The key issue with this report is about trust, because the public needs to be able to trust the industry and we need to be able to trust the government department that is responsible for regulating the industry and every time a report like this becomes known about it just undermines that trust."
Mr Hardstaff said the fact the report had not been officially released showed there was a need for an independent inquiry into MPI and the fishing industry.
"This report is deeply disturbing for a number of reasons and not least because the hoki fishery has been held up as a standard bearer for sustainable fishing in New Zealand. We've got to remember that fishing quota is a right but with rights come responsibilities and the practices that have been set out in this report, these are the opposite of responsible."
But the head of Talley's Nelson division told Morning Report the way it declared its fish catch had changed and it did not under-report.
Tony Hazlett said the information was from six years ago and a lot has changed since then.
Mr Hazlett said mealing machinery on board fishing boats was not used to hide catching under-sized fish.
"No, it is not a way of hiding anything. Having fishmeal plants on board is a way to maximise utilisation of all the offal and everything that comes out of producing fish. You can be very confident that hoki is getting fished sustainably, and we're constantly looking at ways to avoid juveniles."
He said hoki was being fished in a sustainable manner.
"You can be very confident that hoki is getting fished sustainably, and we're constantly looking at ways to avoid juveniles.
"It's a very healthy fishery at this point, and will be for some time."
MPI did not respond to a request for an interview.
A spokesperson for Fisheries Minister Stuart Nash said she had no knowledge of the report's 45 recommendations and that the investigation predated his appointment as minister.