Cranes have started pulling farmed oysters out of the water in Big Glory Bay on Stewart Island in an effort to stop a fatal parasite, bonamia ostreae, from spreading to the wild fisheries in Foveaux Strait.
The Ministry for Primary Industries (MPI) ordered all the oysters be pulled up after finding the parasite on two farms last month.
Caged oysters - the first to be removed - are being lifted out of the water by crane, before being disinfected, wrapped and placed on a barge.
The ministry said the boats themselves would also be disinfected and cleaned before leaving the bay for Bluff, taking a longer route to avoid the wild oyster fisheries.
The oysters would then be dumped and covered, in a Bluff landfill.
MPI spokesperson Geoff Gwyn said earlier that officials and the community were working together to make sure the oysters were removed from the water safely.
"We have acknowledged the strong feeling among locals to act quickly and to minimise the chance of any further spread during the removal process," he said.
One of the affected oyster farmers said he doubted he would ever be able to return to growing the shellfish commercially in Big Glory Bay.
Jeff Walker, who owns two farms, where he grows oysters on ropes alongside mussels, said there was a feeling of resignation among farmers because the cull simply had to happen.
"In every fishery around the world where this particular strain has occurred, it's basically wiped out 90 percent [of the stocks]," he said.
"Although it might be possible to grow, the scientists are saying it's most unlikely you'll ever be able to grow commercially again."
Mr Walker said he expected the mussels on the ropes would not be recovered, and the entire lines - mussels, oysters and ropes - would be disposed of.
It would probably take another four to six years for the bay's mussel farms to recover once those lines had been removed, he said.
The biosecurity compensation for farmers was unlikely to cover future losses, he said.
Meanwhile, there is no timeframe yet for the removal of oyster farms in the Marlborough Sounds. MPI said it was still working with farmers in the area on a timeframe.