The Ministry for Primary Industries is being accused of a double standard in how it deals with biosecurity threats in the water and on the land.

It has ordered the removal of every single oyster from Stewart Island's Big Glory Bay, after the lethal Bonamia parasite was found there last month.

Bluff oysterman Willie Calder said he is glad the ministry is now acting, for the sake of mainland oyster farmers.

But he said he is worried the removal won't actually start until Tuesday, when the ministry has already known about the parasite for weeks.

Calder said if it was a land-based issue, like foot and mouth, MPI would have responded overnight, but in this case the ministry has waited weeks and that's concerning.

READ MORE: Mass cull of Stewart Island oysters

MPI has also ordered the removal of oysters from Marlborough due to a separate parasite which was detected two years ago.

Calder said the decision will be devastating for Stewart Island farmers but could save the industry as a whole.

He said he hopes it won't be too late, because Bonamia can be contagious when infected oysters die, but it's a relief to see the right actions being put in place.

MPI has also ordered the removal of oysters from Marlborough due to a separate parasite which was detected two years ago.