Thousands of tonnes of oysters will be removed from Stewart Island's Big Glory Bay as early as Monday, in a bid to save the Bluff oyster industry from a lethal parasite.

Oyster farmers from Stewart Island and Bluff, representatives from Southland's councils, Ministry for Primary Industries officials and ministry contractors gathered yesterday to formulate a plan for the removal operation.

MPI field headquarters and operations manager Andrew Sander said the plan still had to go to consultation with affected parties, but it was hoped the operation could begin early next week.

"At this stage, the ideal will be Monday, but it may not be Monday because we have a huge number of resources that we need to bring in.

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"I'm talking about equipment and putting processes in place for disinfecting and cleaning, and that's not going to happen immediately.

"It's also weather-dependent."

The move comes nearly a month after the Bonamia ostreae parasite was detected in flat oyster stocks at Big Glory Bay.

Mr Sander said the "best-case scenario" was the operation would take two weeks to complete, but possibly longer.

A minimum of 4000-6000 tonnes of oysters would be lifted in the operation, and would probably be destroyed.

"The parasite is harmless to humans and the oysters are quite edible, but we want a clean operation and a quick operation."

It was not yet known how much the removal would cost."This is a priority for MPI because it is a huge issue for this region.

"As far as we're concerned, we need this operation done so that our farmers can get back to business as usual as soon as they can.

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"The actual cost of the operation is not an issue at the moment. We want this job done.

"We're totally aware that if this parasite spread to the Bluff oyster beds, it would be disastrous," Mr Sander said.

A compensation deal for the farmers was still being worked through, he said.