A Salvin's albatross in full flight as it soars over the Southern Ocean. It occurs only on New Zealand's Bounty and Snares islands.

The fishing industry is under fire for killing endangered seabirds when catching hoki, and overfishing and wrecking the seabed when taking orange roughy.

Environment groups have said the Marine Stewardship Council (MSC), the agency that gives a seal of approval to the industry, is guilty of deceiving the public over sustainability issues in the deepwater fisheries.

The hoki and orange roughy fisheries are two of nine worldwide that have been highlighted by 66 groups for being environmentally destructive.

ROSS GIBLIN/STUFF A vessel fishing for hoki in Cook Strait. There is no link between this boat and albatross deaths.

They have written an open letter to the MSC, calling on it to address the "unacceptable impacts" of fisheries that have received MSC certification or have been re-certified.

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One of the signatories, Forest and Bird, said the Salvin's albatross which is rated as "critically endangered" was being caught and killed during hoki fishing at a higher rate than the population could sustain.

SUPPLIED A Salvin's albatross drowned in a hoki fishing net. The photo was released to Forest and Bird following an Official Information request.

At last count in 2013 there were 39,000 breeding pairs on the Bounty and Snares islands, off New Zealand's southern coast. They are the only places the species occurs.

The huge birds, which breed only every two years, are caught in nets as they dive for fish, and by striking warp lines.

"All seabird deaths in the hoki fishery have continued to increase over the last few years, when they should be declining if fishers were using sustainable fishing practices," Forest and Bird seabird advocate Karen Baird said.

Seafood New Zealand rejects the assertion, saying while there were some deaths, the Salvin's population had grown from 31,000 breeding pairs in 2010 to 39,000 in 2013.

However Baird said the population counts were incomplete and failed to take into account the fact the bird bred only every second year, so it needed more than two year's data to detect a trend.

"Salvin's albatross population declined by 10 per cent in the main population on the Bounty Islands between 2004 and 2011, resulting in their designation as critically endangered in 2013 and again in 2016," Baird said.

Bird counts from the 1970s showed there were 76,000 breeding pairs.

Since large scale trawling of orange roughy started in 1979, the fishery has had a history of depletion and repeated population crashes.

Some of the fish, which live at depths of up to 1.5 kilometres, have been estimated to be as old as 150.

"It is ridiculous that the majority of New Zealand's orange roughy stock are certified as sustainably fished. Their population has been decimated by years of over-fishing, and under reporting of landed catch. Orange roughy is caught by bottom trawling, probably the single worst fishing method, which effectively bulldozes sea floor species and destroys fragile ocean habitats," Baird said in a statement.

The groups which signed the letter to the MSC said there had been known under-reporting and dumping of fish, and misreporting of orange roughy landing data.

They said recent scientific studies had shown that deep-sea bottom trawling was "...effectively irreversible on time-scales of natural ecological processes" and that recovery times for impacted deep-sea life could take "centuries to millennia".

Despite these criticisms, the New Zealand orange roughy fishery was certified in December 2016.

Seafood NZ said the fisheries were reassessed every five years and underwent annual audits to ensure they continued to meet the MSC's "strict standard" and to account for any new information.

Last year a more precautionary approach was taken when reassessing the hoki fishery.

"This is more precautionary than is required by MSC but was put forward by industry who want to ensure they meet the highest environmental standards," Seafood NZ said in a statement.

The latest statistics show hoki exports were valued at $188 million in 2010-11, well down from $346m in 2001 when tonnages were much higher. Forest and Bird said the Fillet 'o' Fish sold at McDonald's in New Zealand was hoki.

In 2014, 2890 tonnes of orange roughy was exported, worth $36.5m, also well down from the $200m at the fishery's peak. Most is exported to the United States and Australia and also sold in New Zealand as frozen fish fillets.