Hector's dolphins are endangered, but not as critically as their relative, the Maui dolphin. The hector population is believed to number around 15,000.
While reviewing the video footage of the dolphin capture, authorities also noticed the vessel's crew discarding numerous healthy fish.
Officials subsequently widened their investigation to five other vessels, four of which were found to be illegally discarding fish in full view of onboard cameras and ministry observers.
No prosecutions were made at the time - a decision which QC Michael Heron criticised today following an independent inquiry.
The inquiry's terms of reference did not cover the dolphin deaths, but MPI said in May it would investigate the issue separately.
WWF New Zealand campaigner Alex Smith said four months on, it was unclear whether MPI had looked into the matter.
"We need to know why that happened and how widespread the problem is," he said.
"If the Ministry knows about dolphin deaths that are caught on camera and is still not reporting these, then what happens when Hector's and Maui dolphins die in fishing nets off camera?"
MPI said the two-year deadline for a prosecution over the unreported dolphin death had passed.
However, the ministry confirmed today that it planned to introduce a standard operating procedure under which MPI must advise of any "non-fish bycatch events", such as dolphin captures.