A Ministry of Primary Industries (MPI) spokeswoman says the 4000 cows on the farms affected by the bacterial disease Mycoplasma bovis will go to the works for food processing as the sickness is not a food safety risk.
An MPI veterinarian will assess the health of each animal prior to slaughter.
"No animals which are sick, severely injured or who have medicine in their system will be allowed to be killed for human consumption - New Zealand law prohibits it," the spokeswoman said.
A small number of animals unfit for transport will be humanely euthanised on site and either sold for pet food or disposed of.
Farmers whose cows are facing the cull can apply for compensation. Compensation will cover verifiable losses relating to MPI exercising legal powers under the Biosecurity Act.