The Ministry for Primary Industries has announced an inquiry into claims it didn't prosecute skippers for dumping fish despite having video footage.
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A leaked ministry report shows its own officials believe this approach is contributing to over-fishing and illegal dumping.
The leaked MPI preliminary report, written by a ministry investigator, looked at video footage on six vessels operating in the Timaru and Ōāmaru ports between November 2012 and March 2013.
The report said MPI's own failure to prosecute skippers was contributing to over-fishing and illegal dumping.
While reviewing the footage, installed as part of a pilot programme, the investigator saw numerous quota species fish, including substantial quantities of elephant fish and gurnard, being discarded.
The ministry will now bring in a top lawyer to examine what went on during operations in the Timaru and Oamaru ports in 2012 and 2013.
The inquiry will also look into a second investigation called Operation Hippocamp, which shows an MPI investigator thought the ministry was putting prosecutions in the "too hard" basket.
MPI's director general Martyn Dunne said that being seen by the public to be holding lawbreakers to account was a high priority.