While New Zealand's most commonly farmed oyster was the Pacific Oyster, there were numerous flat oyster farms around Stewart Island and Marlborough.
MPI acknowledged this "isn't positive news" for affected farmers but said science had strongly guided its decision.
"The epidemiology of Bonamia ostreae, and the proximity of the two affected marine farms to others, means there is a strong risk of spread to those farms, and increasing the threat to the wild population," said MPI readiness and response services director Geoff Gwyn.
"Removing all of the flat oyster stocks from the marine farms in Big Glory Bay significantly reduces this risk."
While MPI appreciated offers of help from locals, Gwyn said the removal of affected oysters without causing further spread was a very particular process and would require expert direction
Bonamia ostreae has been in New Zealand since 2015 in the Marlborough Sounds and Nelson. This is the first time it had been found in another area of New Zealand.
"There is no food safety issue from eating oysters with Bonamia ostreae. Fresh, good quality New Zealand oysters continue to be safe to eat," Gwyn said.
Sampling to date has found no evidence of Bonamia ostreae in Bluff oysters in Foveaux Strait, however, MPI was continuing its sampling and surveillance.
"We have been in contact with the affected Big Glory Bay and Marlborough marine farmers," Gwyn said. "We would like to thank them for their input and cooperation to date.
"We're confident that the movement controls already in place have given us the time to get this next stage right. We will be working closely with the marine farmers to outline the plan for the removal of the oysters."
Compensation under the Biosecurity Act was a matter MPI would be discussing with the affected Big Glory Bay and Marlborough farmers.
