The cull of Stewart Island's caged oysters is under way, about three weeks after a lethal parasite was first detected in the area.

An oyster farm operated by Sanfords in a joint venture with a company called Tio is the first of about six farms in Big Glory Bay, Stewart Island, to have its entire flat oyster stock removed in a bid to prevent Bonamia ostreae spreading to the Bluff wild oyster population.

It is estimated between 120 to 160 cages, each containing about 40 to 60kg of oysters, would be lifted yesterday.

Sanfords was one of two Stewart Island farms where the Ministry for Primary Industries (MPI) found the parasite last month.

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It was the first time it had been found in another area in New Zealand since it was first detected in the Marlborough Sounds and Nelson in 2015. It is fatal to flat oysters, but is not harmful to humans.

So far, extensive sampling has not found the parasite in the Foveaux Strait fishery.

MPI national biosecurity capability network manager Andrew Sander said he was
''absolutely'' satisfied with the timeframe in which action had been taken to prevent the
parasite's spread.

MPI staff had been on the ground in Stewart Island since day one, he said, and there were
many parties involved who needed to be consulted with before a decision could be made.

''We have been pretty quick on this. We want this right the first time.''

Sander said the action to remove all farmed oysters from Stewart Island would not give 100 per cent certainty the risk of the parasite spreading would be eliminated, but it would reduce the risk.

Bluff Oyster Management Company operations manager Graeme Wright said he was satisfied with the speed of the intervention.

''There were huge decisions to be made at that time. While you want it to be as quick as you can, the right decision has been made now and we want to support them to get it done.''

Stewart Island-Rakiura Community Board chairman Jon Spraggon said the decision could have been made sooner.

''It is probably not moving fast enough. Bureaucracy doesn't move fast.''

The effect of the intervention on the community was going to be ''substantial'', but the community was on board with MPI's decision, he said.

''We have to be. It is a crud and we have to do something to prevent it spreading further.''

The caged oysters are being uplifted by crane, then securely transported by vessel and truck to a landfill site outside Invercargill to be buried under lime and dirt to provide protection from vermin and ensure rapid decomposition.

The vessels transporting the oysters are taking an indirect route from Stewart Island to avoid passing near oyster fisheries in Foveaux Strait and sites of significance to local iwi.

Sander said today's operation was a trial run, after which staff would have a better ideaof how long the process would take to complete.

MPI readiness and response director Geoff Gwyn said in a statement it acknowledged thestrong feeling among locals to act quickly and to minimise the chance of any further spread during the removal process.

''Our aim is to complete the work with minimal disruption to the local community.''
MPI staff will be conducting public meetings in Stewart Island and Bluff this week to inform the communities about the plan. Staff were also meeting with the affected farmers yesterday to discuss their compensation claims.

A spokeswoman from Sanford did not return a call yesterday.

- Southland Express