The trawler had just brought a "bag" of snapper on board when three large waves hit the boat, causing the loss of fish and considerable damage to the vessel.
Crew members were all safe but the skipper decided the best course of action was to steam straight back to port, arriving back in Onehunga early this morning.
The loss of fish at sea was regrettable but the skipper acted responsibly and safely, Aotearoa Fisheries chief executive Carl Carrington said.
"The skipper has done everything right," Mr Carrington said.
"Coming straight back to port to ensure the safety of his crew was paramount in this situation. He had recorded the loss on his catch landing report as he is required to do."
The recorded loss comes off the allocated quota and is accounted for under the quota management system, Aotearoa Fisheries said.
Ministry for Primary Industries officials were at port soon after the vessel arrived to undertake an investigation, the company said.
A video showing a trail of dead fish on Muriwai Beach was captured by members of the public yesterday and passed on to recreational fishing advocacy group LegaSea.
The Ministry for Primary Industries said fishery officers rushed to meet the boat when it arrived in port this morning.
Two officers had visited Muriwai beach on Tuesday and confirmed a large number of legal-sized snapper and a small number of gurnard and john dory fish had washed up.
At the same time, officers checked new vessel-monitoring technology and established a trawler that had been working off Muriwai on Monday night was on its way to Onehunga Wharf.
The technology showed an "unusual kink" in the boat's course - which corresponded with the crew's version of events, the spokesman said.
Fisheries officers collected the catch returns for the trip and further information from the boat's electronic equipment for further analysis.
MPI district compliance Manukau manager Jacob Hore said it was great MPI received a call about the unusual fishing activity in a timely matter.
"The person who phoned this in did everything right. Getting accurate information as soon as the fish were spotted meant we could respond immediately," he said.
The monitoring equipment is a joint Government and industry initiative to improve information available for sustainably managing fisheries.
MPI encourages people to report any suspicious fishing activity to confidential hotline 0800 4 POACHER (0800 476 224).