The dumped fish was valued between $800,000 and $1.4 million.
MPI later laid charges against the men under the Fisheries Act 1996 for misreporting and illegal dumping of fish.
Commercial fishing largely relied on the honesty of fishers and fishing companies, said Peter Hyde, the MPI's district compliance manager for Canterbury/Westland.
"In this case there was a serious breach of trust in reporting catches of quota fish species which is very disappointing to see," Hyde said.
"The dumping of damaged and small quota fish allowed the crew to maximise financial return through landing better quality, higher value fish."
An investigation included interviewing the 32 Indonesian crew who had worked on the vessel during the two trips the offending took place.
Six of the Indonesian crew remained in New Zealand to give evidence at a hearing in June this year, Hyde said.
A fifth man, the vessel's factory manager, was convicted and will be sentenced at a later date.
A commercial fisher who unlawfully dumped fish was liable for a penalty of up to $250,000.