The first flat oysters will be stripped from farms on Stewart Island tomorrow.

It's been three weeks since the potentially fatal Bonamia parasite was first found in Big Glory Bay.

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The Ministry for Primary Industries has met with farmers, and they've been given guidelines on how to remove the shellfish.

The caged beds will be uplifted by cranes then transported by boats and trucks to landfill in Bluff.

This is the first time the parasite has been found outside the Marlborough Sounds and Nelson, in New Zealand.

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