Sealord must forfeit a US$16 million (NZ$23.98m) vessel and pay penalties for five bottom trawling incidents in a protected area during 2018 a hoki fishing trip.
The global seafood enterprise must pay $24,000 dollars for the offence, while a vessel master and first mate have also been fined.
Sealord must also forfeit the proceeds from the entire catch - more than $112,000, along with the boat.
According to the Ministry for Primary Industries (MPI), Sealord failed to take reasonable steps to avoid the offending.
"All bottom trawling and dredging is illegal in benthic protected areas," MPI compliance director Gary Orr said.
"To ensure that fishing gear does not touch the bottom, trawling within 100m of the seabed is prohibited within a benthic protection area.
"It is important that the companies sending skippers to sea give them adequate training and provide sufficient oversight well after the vessel leaves the port."
MPI says the fishing trip happened at Chatham Rise, about 200 nautical miles east of Christchurch.
"For each of the trawls, the net was hard on the seabed and within the lower buffer zone of 50 metres off the bottom."
About 40,000 kg worth of fish was caught during the trawls, MPI says.
"Sealord Group Ltd can make an application to the courts for relief from the effects of forfeiture in relation to the vessel," the public service department said in a statement. "The defendants were sentenced on the basis that they had not deliberately bottom trawled in a protected area, but they had failed to take reasonable steps to avoid the offending."