The removal of flat oysters from Big Glory Bay on Stewart Island begins tomorrow.
The Ministry for Primary Industries ordered the cull in a bid to halt the spread of the parasite Bonamia ostreae.
The parasite was first discovered in Marlborough two years ago and last month was picked up on Stewart Island, prompting fears it could threaten the famous Bluff oyster industry.
The Bluff oyster industry has been pushing hard for a complete cull, saying it is the only possible way of stopping the infection from reaching Foveaux Strait.
The Ministry for Primary Industries said the oysters in commercial farms would be collected by crane, and then securely transported by vessel and truck to a landfill in Bluff for disposal.
Precautions were being taken, such as taking an indirect route that bypasses oyster fisheries in Foveaux Strait.
A spokesperson, Geoff Gwyn, said the ministry was continuing to support local farmers affected by the removal.