28 farms were infected by the bacterial infection Mycoplasma bovis, originally detected on an Oamaru dairy farm in July last year.
The Ministry of Primary Industries decided to cull all cattle on the 28 infected farms in a bid to stop the disease spreading.
Federated Farmers National President Katie Milne said the emotional effect of the decision to cull was "horrendous" for farmers. But she said it was the "best shot" New Zealand had at getting rid of the infection.
The Mycoplasma bovis infection has been a learning curve for New Zealand's agriculture industry, she said.
"If there are any disease problems [in the future], we can trace animals faster and that will be a really big boost for our industry once we get that sorted," she said.
"We will have to get our Nait systems on farms up to scratch and this will make us more prepared in the future."
She said the matter is not related to food security and only concerns animal welfare.