The governments has released its plan to contain and eradicate mycoplasma bovis cow disease.
The disease was discovered in July past year and since then 41 farms have been confirmed as infected.
Although many cows are expected to be killed at processing plants and be used for beef, some may have to be killed and buried on farms or in specified landfills, AP reported. Authorities insist the decision is to stop future production losses and is unrelated to food safety.
The decision was taken to "protect the base of our economy - the farming sector", Prime Minister Jacinda Ardern said.
"This is a tough time, and the pain and anguish they're going to go through is really disgusting", she said of the affected farmers.
Eradication has meant the culling of thousands of cows, especially in the dairy industry. Until July New Zealand was one of only two major OECD dairying countries that were free of the disease.
She said the cull, the majority of which would take place over the next two years, would aim to eradicate the disease completely.
Already, 26,000 cattle have been destroyed in the 10 months since the disease was first recorded in New Zealand.
According to reports, the officials in New Zealand have the right to kill the cows and enter any farm if they doubt that the farm might be affected.
Federated Farmers National President Katie Milne said the process represents a "rough time" for the farmers, adding that they "have to support them as neighbours, community members, farmers, friends".
"This is a necessary, unfortunate part of not having yet a test that clearly identifies the individual animals", he said. "But the alternative is to risk the spread of the disease across our national herd".
An investigation into how Mycoplasma bovis got into the country is still underway.
If all goes as hoped with the slaughter, New Zealand would be the first country to have registered an infection and successfully remove Mycoplasma bovis from its herds.
Officials say they expect to know by the end of the year whether the eradication plan is working.