Graeme Wright, of the Bluff Oyster Management Company, welcomed yesterday's announcement but told the Otago Daily Times it was "most likely to be the end of flat oyster farming in Big Glory Bay".
Scientific evidence overseas suggested the parasite returned whenever the oyster farmers did, even a decade later, he said.
"It's really harsh on those guys. I do feel for them. I know some of them personally and certainly down here, they're part of the wider community.
"But at the end of the day my job is effectively to save the Foveaux fishery."
Oyster farmers from Stewart Island were still digesting the news yesterday, including Joe Cave, the managing director of Southern Seafoods.
He said his company was affected "probably more than anybody", but he declined to comment until after next week's meeting with MPI officials.
A spokeswoman for Sanford, involved in a joint-venture oyster farm at Big Glory Bay, said the company would do "whatever MPI requires of us".
The company would wait to hear from MPI next week on how the removal would be conducted, but in the meantime it sympathised with other farmers affected by the decision, she said.
Yesterday's developments came a day after Mr Wright criticised MPI's handling of the Bonamia ostreae parasite's discovery as "incompetent".
The parasite was first found in the Marlborough Sounds in 2015, but MPI had failed to act on international scientific advice, received in mid-2015, which recommended removing all infected oysters to minimise the risk of it spreading.
Yesterday's decision to lift contaminated oysters in Marlborough - as well as those in Stewart Island - was "probably what should have happened two years ago", Mr Wright said.
Mr Gwyn reiterated MPI had acted on the "best available information" at the time, including scientific advice, geographic proximity to wild oysters, tidal currents and the impact on the industry and communities.
Mr Gwyn did not respond directly when asked if the decision not to lift the oysters sooner had turned out to be a mistake.
The industry has also reiterated oysters remained "100% safe" to eat, despite the parasite's presence, raising the prospect of a possible glut on the market.
Mr Gwyn said he could not say how many oysters might be removed, or how long the work could take, until after next week's meeting.
MPI was also still assessing whether mussels mixed with oyster farms would also need to be lifted, he said.
Farmers would have to apply for compensation from MPI, which would also cover the cost of the removal operation, but "we don't want to speculate on a figure", he said.
"We will be talking in detail with affected farmers about how this process works next week."
Mr Wright said the industry had worked hard to protect the Bluff oyster fishery, but that work would be in vain if the parasite spread across Foveaux Strait.
That was despite the presence of an "endemic" but less destructive strain of the Bonamia parasite, Bonamia exitiosa, and "huge ups and downs" in the industry.
"To date, whether it's been through good luck or good management - I'm not sure - but we still have a commercially viable fishery.
"To have a concurrent infection, with both those parasites operating, the likely outcome is doom."
