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The Ministry for Primary Industries announced yesterday it would begin a cull of 22,332 cattle today on all infected sites after scientific testing and tracing confirmed the disease was not endemic.
It was working immediately with farmers to kill the stock on the 22 active infected properties which still contained cattle, it said.
The disease can cause pneumonia, abortions, lameness and mastitis and can result in the deaths of infected cows.
Federated Farmers North Otago dairy chairman Lyndon Strang said the cull would be "the right thing'' for New Zealand agriculture.
"It's a really unfortunate position for those farmers that are in those infected properties and I just really hope that the compensation process happens quickly.''
The Government approved $85 million in funding for operational and compensation costs for the outbreak response earlier this month, adding to the $10 million approved in December.
About $60 million of that sum was earmarked for compensation.
Farmers in general were supportive of the cull, Mr Strang said.
Those with infected stock would need a lot of moral support from other farmers, he said.
"Your livestock is part of your farm - it's something you do get close to.''
VetSouth director and co-founder of Mycoplasma Bovis Action and Support Southland Mark Bryan, of Winton, said even farmers whose cattle were infected knew a cull was necessary.
"It's very hard to treat and it spreads very quickly. If it makes its way into a herd, within a year the whole herd will have it.''
The disease has been detected on farms in North Otago and Middlemarch, several sites in Southland and Canterbury, and one near Hastings.
Federated Farmers Southland president Allan Baird said he was pleased, from an industry perspective, the Government had made a decision in a "timely fashion''.
"Even though that's going to be very difficult for the farming families and businesses whose stock will be moved to slaughter.''
Farmers recognised compensation would be a long process, but it would be "of value'' if the ministry could make partial payouts in the meantime, Mr Baird said.
The MPI had estimated the cost of the disease to the economy at between $60 million and $400 million over the next 10 years, NZME reported yesterday.
MPI response director Geoff Gwyn said the ministry was working with farmers on how the cull would occur.
The "depopulation'' of infected herds was a critical measure to control the spread of the disease, he said.
The testing of milk from every dairy farm in New Zealand was "very well advanced'' and to date had identified only one new infected property, he said.
Non-infected farms under restricted places notices or notices of direction were not asked to cull herds at this point, he said.
Everyone wanted to eradicate the disease, but it had to be technically possible, practically achievable and affordable for everyone, he said.
Agriculture and Biosecurity Minister Damien O'Connor said culling the cattle would give farmers "much-needed certainty'' as to their futures.
"It has taken some time to get to this point. The previous National government ignored the known deficiencies of the NAIT [national animal identification and tracing] system and was slow to react to the initial discovery of Mycoplasma bovis.
"Work continues to determine whether we can eradicate or move to long-term management of Mycoplasma bovis.''
Mr O'Connor confirmed the cull was under way on Tuesday.