The Ministry for Primary Industries has admitted it's unsure how long it will take to remove tonnes of oysters potentially infected with the Bonamia oestreae parasite in Big Glory Bay, Stewart Island.

Work has begun to remove what local farmers believe could be more than 4000 tonnes of oysters, to contain the spread of the deadly disease.

Ministry staff were on hand to watch local farmers and fishery staff remove dozens of oyster crates from Sanford's fisheries this morning.

The cages are being lifted on to the company's barge, before being hoisted on to a freight ship.


A chlorine solution is then applied to the cages to ensure they are cleaned.

A shroud has been placed between the two vessels to ensure drips re-enter the water.

MPI's Southland field operations manager Andrew Sander said there was no timeline set for the complete cull.

"Today's a big operation. We'll be able to gauge how long it may take," Sander said.

"Certainly we hope by the end of today or tomorrow we'll have a better indication of how long it may take."

Around 180 cages worth of oysters will be on each freight boat trip to Bluff. From there they will be transferred to a landfill near Invercargill where they will be covered in lime and dirt. In total, about 4000 tonnes of oysters are due to end up in the dump.

The operation comes almost a month after the parasite was first found in two Big Glory Bay farms during routine checks. It was also 10 days after the Ministry ordered farmers to cull all oyster fisheries in the area, as well as in Marlborough where stocks were decimated by the parasite in 2015.

Sander emphasised MPI staff had been on site "from day one, but said there may be lessons learned.


"It's also important to realise this is not a small operation. The planning stages of this is quite significant and in order for us to achieve what we want to achieve, which is a quick and smooth operation in order for the farmers and the island people and Bluff people to get back to some sense of normality, we've had to plan it down to the finest details.

"At the end of the operation there'll be an extensive debrief. That will have us looking at ways to improve our processes and looking at ways to perhaps quicken up our processes."