A New Zealand fishing company faces the forfeiture of a $20 million trawler after being caught fishing in a protected zone.

Sanford Ltd, and two employees, skipper/master Grant Walker and first mate William Lash, used trawl nets on several occasions in a Benthic Protection Area (BPA) in New Zealand seas in 2017 and 2018.

The company, along with Walker and Lash, have pleaded guilty to breaches of the Fisheries Regulations and are being sentenced at Christchurch District Court.

Sanford is the registered owner of the 64m deep-water stern trawler San Waitaki which primarily targets orange roughy, oreo dory, hoki, and squid in New Zealand waters, mainly around the South Island and Southern Ocean.

In 2005, the seafood industry, through the Deepwater Group, of which Sanford is a member, proposed that the Government establish a series of BPAs that would prohibit bottom trawling and dredging across a broad range of deepwater benthic habitats.

It came after concerns about the impact of bottom trawling on benthic communities.

Species like corals and sponges are highly vulnerable to damage caused by bottom fishing, according to MPI, especially bottom trawling, where heavy fishing gear is dragged over the seabed.

Scientists predict it could take decades, even centuries, after fishing has stopped for some deep-sea benthic environments to recover.

In 2007, New Zealand established BPAs under the Fisheries Act 1996 to set aside 17 large areas covering 1.1 million square kilometres of largely pristine seabed – about 30 per cent of the country's seabed, an area four times the landmass of New Zealand – which protected them against dredging and bottom trawling.

The court heard that between October and November 2017, and October and November 2018, Walker and Lash bottom trawled within the lower buffer zone of the Puysegur BPA – an area of 80 square nautical miles located approximately 70 nautical miles west of South Cape on Stewart Island.

On both trips, 50-year-old self-employed fisherman Walker and Lash, 45, trawled along the Puysegur BPA seabeds on several occasions.

Later when Walker was spoken to by authorities, he admitted the illegal activity, saying he thought the relevant BPAs had been put into the vessel's Sea Plot computer system.

Lash said he didn't think they had been within a BPA at the time they were fishing.

Sanford, which has no record of previous fisheries offending, said they relied on the professionalism of the master and crew of their vessels to follow company instructions and be familiar with all the relevant laws.

MPI told the court that any breach of BPA regulations "undermines the efforts of industry to protect the marine environment" and may impact on the "acceptance and access of New Zealand fish products" in offshore markets.

Under New Zealand law, any proceeds from the sale of fish and "any property used in respect of the commission of the offence" is automatically forfeited to the Crown under the Fisheries Act "unless the court is satisfied there are special reasons relating to the offence".

The court heard that the San Waitaki, which is valued at $20m, should now be forfeited to the Crown, along with $150,000 of fish taken in the Puysegur BPA in 2018.

Lawyers for Sanford are arguing that there are indeed special reasons which mean the vessel should not be forfeited.

The company, and Walker and Lash, also face fines of up to $100,000.

Judge Stephen O'Driscoll has been hearing lawyers' submission today.

The judge has indicated that he will reserve his sentencing decision to a later date to allow time to consider what outcome he will reach.