Bluff oyster lovers can breathe easier - the disease that hit oyster farms on Stewart Island looks to have been contained.

The Ministry for Primary Industries (MPI) last month culled stocks of flat oysters in Stewart Island's Big Glory Bay after two marine farms there were found to be infected with the parasite Bonamia ostreae.

Removal of the last of the caged oysters finished over the weekend in Big Glory Bay. This week MPI is pulling up ropes on which oysters are also grown.

Bluff oysters are the same species but are harvested wild, using dredges, in nearby Foveaux Strait. MPI said no Bonamia ostreae had been detected in the Bluff wild oyster fishery following tests.

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"This is good news and demonstrates that the removal of farmed oysters from Big Glory Bay is the right thing to do to lessen the risk to the wild fishery," said MPI's director of readiness and response Geoff Gwyn.

"We sampled 11 locations across Foveaux Strait and bonamia was not detected in any of the samples," Gwyn said.

"The testing gives us 95 per cent confidence that bonamia is not present."

MPI had also recently carried out testing in farms and a hatchery in Horseshoe Bay, a hatchery in Bluff harbour and in Bluff harbour itself. No bonamia ostreae had been detected in any of these areas, he said.

Since March last year, MPI has conducted six-monthly sampling and testing of farmed and wild oysters for Bonamia ostreae in Marlborough, Otago, Chatham Islands and Southland.

The surveillance programme was designed to detect early infections, so that measures could be implemented to control the spread of disease.

MPI said it would continue with the removal of farmed oysters in Big Glory Bay, and the Marlborough Sounds, as planned.

The ministry removed the last of the caged oysters over the weekend at Big Glory Bay.

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Operations get underway in the Marlborough Sounds this week.

Gwyn said he was grateful for the cooperation of the oyster farmers and the community in the process "which we know is challenging for them".

Because of the proximity of farms and tide and current movements, Big Glory Bay is being treated as a single "epidemiological unit" - which means that every oyster within the bay is assumed to have been exposed to the disease.

MPI will continue to actively monitor the wild fishery and the next round of sampling and testing will be conducted in September, he said.

The Bluff wild oyster fishery alone is worth about $20-25 million a year and directly employs about 250 people.

Graeme Wright, operations manager for the Bluff Oyster Management Company - which represents stakeholders in the fishery - welcomed the news from MPI.

"It was certainly the answer that we were hoping for," Wright told the Herald.

"You can only take the best advice - based on overseas experience and science. As an industry we are very pleased that they have done it."

He said the news from MPI was a "fantastic starting point".

"It is a pretty close knit community in Bluff and Stewart Island so we feel sorry for the farmers affected down there," he said.

Wright said the value of the fishery went beyond dollars and cents.

Bluff oysters are an important seafood among iwi, he said, and the annual Bluff Oyster Festival attracts charter flights from Auckland and Wellington.

"It puts Bluff and Stewart Island on the map," Wright said.

In the past 40 years aquaculture in New Zealand has grown from small beginnings to a significant primary industry.

In 2016 New Zealand's aquaculture sector generated more than $500m in revenue and employed more than 3000 New Zealanders.

In the late 1980s, the Bluff wild oyster fishery was hit by the parasitic protozoan Bonamia, forcing its closure in 1991.

Harvesting resumed on a limited scale in 1994, after which quotas were gradually increased as the fishery recovered.

The Bluff oyster season runs from March through to August.