Benthic protected areas are intended to protect vulnerable species on the seafloor. Seventeen areas were declared in 2007, protecting 1.1 million square-kilometres of seafloor.
"All bottom trawling and dredging is illegal in benthic protected areas," ministry compliance director Gary Orr said in a statement. "To ensure that fishing gear does not touch the bottom, trawling within 100 metres of the seabed is prohibited."
Orr said it is important that companies sending skippers to sea give them adequate training and provide sufficient oversight well after the vessel leaves the port.
Sealord chief operating officer Doug Paulin said that despite the incident being due to unintentional human error, the company pleaded guilty and was convicted as the offences under the Fisheries Act 1996 come with strict liability.
There was no financial benefit to the firm, as the proceeds were handed to the Ministry for Primary Industries.
"While we are disappointed with today's outcome, as we believe we did everything we reasonably could have done to prevent this incident occurring, we respect the court's decision," he said in a statement.
"As Ocean Dawn has been forfeited to the Crown, we will now apply to the court to have the vessel returned to us. In the meantime, we are permitted to use her in the normal course of our fishing operations."