To prevent further spread, about 4000 cattle needed to be culled and the properties decontaminated before the farms were repopulated.
A small number of animals had already been culled on the farm in the Oamaru area and the North Canterbury property and no cattle remained on those properties.
All premises, transportation vehicles and equipment involved in culling would follow a strict decontamination and disinfection protocol to mitigate the risk of spreading the disease.
Once the cattle were removed, there would be at least a 60-day stand-down period when no cattle would be permitted on the farms. During that time, the properties would be cleaned and disinfected. Following that, the aim was to get cattle back on the farms as quickly as possible and surveillance, monitoring and testing would remain in place as a further safeguard.
The affected farmers could apply for compensation for verifiable losses relating to MPI exercising legal powers under the Biosecurity Act.
Van Leeuwen Dairy Group is a high-profile operation founded by Aad and Wilma van Leeuwen and includes the world's largest robotic dairy barn.
Mr van Leeuwen could not be contacted yesterday.Mr Gwyn said MPI would work closely with animal industry bodies, the Rural Support Trust and others to support the affected farmers.
Federated Farmers supports the cull - national president Katie Milne said it was the only option which would ensure peace of mind for the rest of New Zealand's dairy and beef farmers.
"This is a disease that we definitely don't want and we should seek to eradicate it, if feasible," Ms Milne said.
North Otago Federated Farmers president Simon Williamson said the decision showed MPI was taking positive action.