The Ministry of Primary Industries was "flawed" in making its decision not to prosecute commercial fishers despite internal reports and video footage of dumping, an independent investigation has found.

But ultimately the decision to let skippers off with a warning was understandable because the matter was complex and all parties co-operated, an independent report by Michael Heron, QC, has concluded.

"I have found no evidence in my discussions of a systemic problem with the prosecution process at MPI," he told reporters today.

LISTEN ABOVE: Forest and Bird's Kevin Hackwell speaks with Larry Williams about the report

The investigation looked into three operations by MPI between 2003 and 2013 and was the most damning in relation to 2012's Operation Achilles.

Monitoring cameras were placed on six set net commercial vessels in a pilot programme to monitor Hector's dolphins, but also recorded discarding of quota fish by five crews.

The skippers were let off with a warning.

"The decision to warn was meant to be combined with 'drawing a clear line in the sand'," Mr Heron found.

"This does not seem to have been achieved. Some steps have been taken but the situation as to discards remains confused."

MPI says the decision was, in part, due to confusion about whether the camera footage could be used in prosecutions and that some crews believed they had immunity because the cameras were not intended to catch illegal activity.

MPI Director-General Martyn Dunne admitted the process failure was "regrettable" but the confusion had now been cleared.

Video cameras have been rolled out on every vessel in the Snapper One fleet off the north east coast of the North Island with the explicit rule that MPI can prosecute for any illegal activity captured.

The rule is expected to be extended to encompass all vessels with MPI cameras.

Non-prosecution was also deemed understandable in relation to Operation Overdue in 2003 which suggested the catch landing record had understated the weight of fish on two vessels and Operation Hippocamp in 2013 which uncovered limited results about the extent of dumping and high-grading in the South-eastern trawl and set net fishery.

Mr Dunne said MPI had started introducing new prosecution decision processes, resulting in 300 prosecutions a year since 2013.

More work is also underway to address the ongoing issue of illegal discarding, including the new Integrated Electronic Monitoring and Reporting System which Mr Dunne said would "revolutionise" fisheries management and provide high level evidence to support future prosecutions.

"This system will mean being out of sight of land will no longer mean being out of sight of MPI," he said.

What they're saying about the independent review into MPI's decision not to prosecute for illegal fish dumping:

"The decision not to take prosecution action and in particular the process leading to it was flawed. The decision however was understandable and available in the circumstances." - independent investigator Michael Heron, QC

"We have already taken action to address some of the underlying issues and I will ensure that MPI takes further swift action to address outstanding matters identified in the report." - MPI Director-General Martyn Dunne

"Mr Heron's report highlights some serious issues that need to be addressed promptly." - State Services Commissioner Peter Hughes

"I'm disappointed with the flawed processes revealed. Mistakes were clearly made and this should not have happened. It is important to note the review found MPI acted in good faith, its processes are robust and its people experienced and professional." National Primary Industries Minister Nathan Guy

"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." - Forest and Bird advocacy and campaigns manager Kevin Hackwell

"The Heron Report is indicative of a much wider cultural problem within MPI, and with the Minister's and MPI's management of the fishing industry. There needs to be a much wider inquiry into fisheries management and the industry's influence over MPI." - Green Party primary industries spokeswoman Eugenie Sage

"It is obvious that the creation of the MPI 'super ministry' has been a failure for the fishing sector. MPI is underfunded and underperforming, drowning in bureaucracy and lacking true leadership from the minister." - Labour Fisheries spokesman Rino Tirikatene.

"If New Zealanders are wondering why it is so hard to catch fish these days, this report offers a simple cause, MPI is helping the fishing industry to cover up illegal systematic dumping of fish." - Greenpeace executive director Dr Russel Norman