Orange roughy is being sustainably fished, says the Ministry of Fisheries, despite two international retailers stopping selling the fish due to concerns over its low numbers.

Greenpeace had called for the Government to put a halt to fishing orange roughy, which was caught by bottom trawling.

Three of the eight stocks in New Zealand waters where the species is caught have been fished to collapse and closed after numbers reached critical levels, Greenpeace New Zealand oceans campaigner Karli Thomas said.

"The rest of the world is saying 'no thanks' to our unsustainable seafood, but our Government insists on continuing to exploit it."

Last week Trader Joes, a United States chain with more than 300 supermarkets, confirmed it had stopped sales of orange roughy "based on customer feedback and in support of work to source sustainable seafood".

Last month Canada's largest retail chain, Loblaw, confirmed it had stopped stocking the fish, Ms Thomas said.

"While we continue to fish using destructive fishing methods and pretend the quota system takes care of everything, our industry and officials will increasingly find themselves in damage control mode internationally.

"New Zealanders are being short-changed by our government and our supermarkets when it comes to seafood. Sustainable seafood policies make environmental sense, and they make economic sense, in both the short and the long term."

But the ministry today said fish stocks were carefully managed to ensure sustainability, using a world leading quota management system.

"Bottom trawling is the main fishing method for catching orange roughy. It takes place within New Zealand's comprehensive fisheries management system," ministry deputy chief executive Gavin Lockwood said.

"New Zealand bottom trawling is very closely managed, we know which fishing vessels are bottom trawling, we use satellite monitoring so we know exactly where they are fishing and we require detailed catch reports so we know how much is being caught."

Seventeen areas have been closed to bottom trawling, providing protection to an area of seafloor equal to 1.2 million square kilometres, or an area four times the landmass of New Zealand, Mr Lockwood said. These were the largest closures of their type anywhere in the world, he said.

"One point two million square kilometres of pristine, un-fished seafloor is protected to ensure that the natural bio-diversity and eco-systems are preserved," Mr Lockwood said.

New Zealand's Quota Management System was internationally regarded as one of the world's best fisheries management systems, he said.

Since the start of 2009 four Canadian supermarket chains have stopped selling orange roughy and one has removed hoki from sale.

Last year Waitrose, the United Kingdom supermarket chain used by the royal family, announced it no longer stocked New Zealand caught hoki as it failed to meet the store's sustainability policy prompting headlines reading "No hoki for Queen".