A rogue rabbit virus, confirmed in Otago, could thwart regional council plans by making the animals immune to its infection operation.

Council chief executive Sarah Gardner says said the RHDV2 virus, previously confirmed in the Bay of Plenty and Marlborough, has been detected in Central Otago through testing by the regional council.

This has been a concern as it could create immunity among the animals to the RHDV1 "K5" virus it released in March in a widespread rabbit-cull operation.

In a statement, Gardner said the council reminded all landowners it was very important to continue rabbit controls in addition to the K5 virus.

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In an email sent to councillor Graeme Bell, Gardner said staff did not know how widespread the virus was or what the level of infection was in the population.

A "more comprehensive report" would be presented to councillors at the next committee meeting in late January.

Bell said the council needed data and information to sort the issue.

"We need to be proactive."

The council was "well aware" it could create immunity to the council-released virus, he said.

The council needed to provide information to farmers about the success of the K5 virus, as many thought it was not working.

When the Ministry of Primary Industries was asked about the RHDV2 virus entering Otago, a Biosecurity New Zealand spokesman said it encouraged pet rabbit owners to take practical steps to protect their rabbits.

"Vaccines are available through veterinarians. This strain is established in New Zealand.

"RHDV2 cannot be eradicated or contained now that it has been confirmed in wild rabbits on both the North and South Islands."