A "damning" report into fish dumping is being seen as clear grounds to take the management of New Zealand's fisheries off the Ministry for Primary Industries entirely.

An inquiry led by QC Michael Heron says its decision not to prosecute commercial operators who were filmed dumping tonnes of healthy fish was "flawed".

It found MPI obstructed the prosecution process, that its decision process was "confused", and that it failed to follow up and "draw a clear line in the sand" over fish dumping.

However, the limitation period for prosecution has now passed.

Spokesman for recreational fishing group LegaSea, Scott Macindoe, said the report was damning.

"Senior Ministry officials allowing the commercial sector to commit some pretty heinous offences, and sweep it away out of sight. It just doesn't get any worse."

LegaSea wants a Commission of Inquiry - and for the Minister to address the situation with a view to taking management of the fisheries off MPI entirely.

"We believe a better structure has to be introduced than the Quota Management System which has been touted as world class but is built on the assumption that MPI was a competent steward for our fisheries," Macindoe said.

"Instead, we are plagued with an industry rife with charges of slavery, dumping, misreporting and political interference, and a Ministry that simply refuses to acknowledge the degree to which it has been captured."

Greenpeace also called for a Commission of Inquiry.

"You have to ask, what MPI are hiding from us. Nothing short of a dramatic shakeup of the MPI fisheries can restore public confidence in the management of fisheries in New Zealand," said Executive Director Russel Norman.

"The report shows that MPI is working for the fishing industry, not for the people of New Zealand. MPI has been caught by the fishing industry - hook line and sinker."

Forest and Bird said the review confirmed the Ministry was in bed with the fishing industry and failing to ensure commercial fishing is sustainable.

"The purpose of the ministry’s fisheries section is to protect the public interest, not to promote the interests of the fishing industry," Advocacy and Campaigns Manager Kevin Hackwell said.

"The ministry has to change its culture to do what it was set up to do – ensure the health of the marine environment and secure the long term future of the fisheries for all New Zealanders."

MPI director-general Martyn Dunne said he accepted the inquiry's findings, which he described as "regrettable".

"It is also disappointing that the process was characterised by confusion and a lack of adequate documentation and communication," Dunne said.

However he said there was no value in blaming the individuals involved and it was "time to move on".

Two senior staff who were at the heart of the investigation had recently moved on to other public sector jobs, but Dunne said this was purely coincidental.