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Council chief executive Sarah Gardner yesterday said the RHDV2 virus, previously confirmed in the Bay of Plenty and Marlborough, was 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, Mrs Gardner said the council reminded all landowners it was very important to continue rabbit controls in addition to the K5 virus.
In an email sent to Cr Graeme Bell, Mrs 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.
Cr 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.
Cr Bell 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 were 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."