Fisheries officials are trying to stop a parasite lethal to oysters from spreading across Foveaux Strait from Stewart Island.
Bonamia ostreae has turned up at two oyster farms on Stewart Island.
The strain first appeared in Marlborough Sounds two years ago, but this is the first time it has been found in another area in New Zealand.
Ministry for Primary Industries biosecurity surveillance manager Brendan Gould said the fear now was that the parasite could spread to wild Bluff oysters in Foveaux Strait.
"We're resigned to the fact it's here. We're not going to stop it from being here - we don't believe that eradication is something that is able to be done.
"Our focus was to try and stop it spreading and we do have controlled area notices in place limiting movement of flat oysters."
Serean Adams, aquaculture manager at Nelson's Cawthron Institute, said the parasite posed a substantial threat to flat oysters, but overseas research suggested selective breeding could help their resilience to pathogens.
Dr Adams says the research institute was well placed to respond to the parasite. It was working on a research strategy document for the New Zealand flat oyster aquaculture industry.
A related strain of bonamia devastated the Bluff oyster industry in the early 1990s, and again in the early 2000s.