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.