Events leading up to the inquiry
The inquiry, led by QC Michael Heron, said the 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" with regard to fish dumping.
Today, Guy said he agreed with the findings.
"It was a flawed process, very poor communication back to the fishers as to why the cameras were on there. So I'm very disappointed that they decided not to go for a prosecution.
"In this one particular case I am disappointed. The director general is now making a raft of changes within MPI in terms of different processes and procedures to ensure this doesn't happen again."
Despite the changes - including fast-tracking more electronic monitoring equipment on boats - Guy said MPI did a very good job and the public could have full confidence in their fisheries enforcement.
"I have trust in MPI because, by and large, they do a good job as the regulator. But you need to understand...dumping and discards has been an issue [they] have been grappling with for a long period of time."
The ministry-commissioned inquiry was launched in May following reports that MPI had chosen not to prosecute local fishing captains who were caught on CCTV cameras dumping healthy-sized fish.
Heron looked at three separate investigations into dumping in 2003, 2012 and 2013, known as Operation Overdue, Operation Achilles and Operation Hippocamp.
Operation Achilles, in November 2012, discovered that five out of six vessels operating off the eastern coast of the South Island had discarded quota fish - mostly gurnard and elephant fish. Between 20 per cent and 100 per cent of quota fish were being thrown out with every haul.
However, despite a recommendation by the investigator, MPI did not proceed with a prosecution and instead issued a warning to the boats' skippers.
This decision, and the process leading up to it, was flawed, Heron's report said.
An internal email written by MPI's director of fisheries management, and released as part of the report, stated, "fish dumping is so widespread that the current system is failing and officials have not been able to get on top of it from day one of the quota management system.
"We estimate that if we found the golden bullet to stop discarding, we would probably put over half of the inshore fleet out of business overnight."
Guy has said that view was a personal one and was not backed up by evidence.