One of our best-loved delicacies is under threat from a virulent parasite.

There are fears that the parasite found in oysters farmed off Stewart Island could cause the demise of the Bluff oyster.

The Ministry for Primary Industries (MPI) yesterday announced it was culling all stocks of flat oysters in Stewart Island's Big Glory Bay after they were found to be infected with the parasite Bonamia ostreae in two marine farms.

The Bluff oysters are the same species but harvested wild from the Foveaux Strait, perilously close to the affected farms.

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The popular and expensive delicacies can be bought at fish and chip shops for a few dollars but at upmarket restaurants like Auckland City's Soul Bar and Bistro cost $6.50 each or more.

While the parasite is not harmful to humans, Bonamia ostreae is deadly to oysters and in 2015 killed over 90 per cent of Marlborough's farmed flat oyster population, according to MPI and a local Bluff oyster expert. It also affected a Nelson aquaculture research facility.

Graeme Wright, operations manager for the Bluff Oyster Management Company, which manages the area's wild fishery, said locals were holding their breath that the parasite did not spread into the strait as the implications would be devastating.

"If it got into our fishery it would probably spell the end. It would lock the door and throw the key away," he said. "It's extremely worrying."

"The social and economic benefits of Bluff oysters, you can't measure that. It's extremely important to the local community, it's hugely important to iwi - oyster, tio, is the king of the table - and the wild fishery has a value to the local economy of probably $25 million a year."

For the Stewart Island farmers that were affected - and the island community as a whole - it would of course be life-changing, too.

"Aquaculture is obviously a big part of their employment base," he said.

Bonamia ostreae only affects flat oysters and when it finds large concentrations of the shellfish the parasite "spreads like wildfire", Wright said.

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Should it make its way to the wild oysters beds "nothing" could be done.

"There's no magic pill," he said.

Wright questioned why MPI had not culled the flat oysters that had all but destroyed the Marlborough industry in 2015.

"All the international literature and all the international science they got was that the only way to minimise the spread of the disease to other New Zealand wild stocks was to remove those oysters from the water for ever.

"They haven't taken that advice for whatever reason - I'm sure they had good reasons for it - but bingo, two years later the Bonamia ostreae strain has been found on farmed oyster sights in Big Glory Bay, which is a hop skip and a jump from the Foveaux Strait wild fishery."

MPI today announced it would also destroy what was left of Marlborough's flat oyster population, despite not having taken this step in 2015.

The Ministry's readiness and response services director, Geoff Gwyn, said any remaining Marlborough flat oyster farmers would receive a notice on Monday requiring them to remove all of their stocks from the water.

He said the decision not to do this two years ago was because it was believed the parasite could be contained by other means.

"The decision taken at the time was to put a controlled area in notice in place and to put in a permitting process. We conducted surveillance and testing in Nelson, Marlborough, the Chatham Islands, Otago and Southland. It's that regular testing that actually identified the two finds in Big Glory Bay," he said.

The discovery of the parasite in Stewart Island oysters was "a game changer".

"I've got to be crystal clear, there is no zero-risk option here when dealing with a marine pest in an aquatic environment which gets moved around by tide and current. We cannot eradicate it, the best risk mitigation is to remove the bulk of the disease from the water."

He acknowledged that if the parasite spread to the wild oyster beds it could kill the Foveaux Stait Bluff oyster.

"Clearly that is the worst case scenario but we believe that what we're doing is going to mitigate that risk."

Gwyn said he had personally contacted the Stewart Island oyster farmers who were affected. He said they were devastated but ultimately saw that it was for the greater good.

"Although it's personally very difficult for them they could see the national good aspect here. So I take my hat off to them, given their own personal circumstances."

MPI was having discussions with them about compensation options under the Biosecurity Act.

One affected Stewart Island farmer, who asked not to be named, said he would soon be forced to destroy the oysters he had cared for and tended to for years.

"It is going to be a serious event and it probably will go further than Big Glory Bay. We think the [preventive] moves are probably a futile act," he said. "We're anticipating that it'll probably be too late to prevent it getting into the Foveaux Strait fishery," he said.

"It's going to be serious; not just for me but for everyone involved, and for the wider Stewart Island community."

His said his livelihood was gone and he felt "numb".