The Mycoplasma bovis outbreak was the "rainy day" the government was planning for, Ardern said.
"If we don't take this one chance, the disease will spread and the risk of it eventually affecting many of our herds is high", Poel wrote in a statement for DairyNZ.
Mycoplasma bovis was first detected in New Zealand in July past year, and manifests in mastitis in cows, severe pneumonia, ear infections and other symptoms.
The bacterium causes illness in cattle, including udder infections, abortion, pneumonia and arthritis. The bacteria is not a threat to humans, but can cause production delays on farms. Some of the slaughtered cattle may be used for beef, but others will be buried on farms or in landfill.
Katie Milne, the national president of the advocacy group Federated Farmers, insisted that authorities would try to make sure affected farmers had all the support they needed, including adequate compensation.
"No one ever wants to see mass culls". They support farmers with information and advice on the practical aspects of the controls.
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New Zealand police have launched a combined investigation with the Ministry of Primary Industries into how the disease made its way to New Zealand, and leapt between the two islands. The dairy herd of the country reportedly has around 6.6 million cows.
New Zealand is known to be the biggest dairy exporter all over the globe and produces near about three percent of the total milk produced in the world.
New Zealand has already culled 26,000 cattle in the 10 months since the disease was discovered. The country will spend 886 million New Zealand dollars (Rs 4,150 crore) over two years on the effort to eradicate the disease.
1 NEWS visited a Canterbury farmer hugely affected by the cattle cull, announced by the government yesterday.
"But the alternative is the spread of the disease across our national herd", Ardern said, adding that it was vital to protect farming, a key sector of New Zealand's economy.
"The majority of animals that we do cull in New Zealand are all healthy".