The parasite detected in two Stewart Island oyster farmers could have an impact on the industry but so far it hasn't been found in wild fisheries, Primary Industries Minister Nathan Guy says.
Bonamia ostreae can be fatal for flat oysters but the parasite doesn't pose a food safety issue.
Mr Guy says bonamia has been around since the 1960s but this is a slightly different strain.
"It's unfortunate, it will have a bit of an impact on the oysters that are farmed on Stewart Island and a controlled area notice has been put in place," he told reporters on Thursday.
"It hasn't been found in the wild fisheries around Bluff, which is really important - we will do what we need to do on the back of good science."