An investigation by Newshub Nation has found serious issues with the response to the Mycoplasma bovis infection.
There were problems keeping track of the diseased herds and the treatment of farmers and in one case, the Ministry for Primary Industries (MPI) has been forced to apologise to a Canterbury couple.
Indecision from MPI over the management of M bovis has driven dairy farmer Amanda Ferguson to breaking point.
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"You don't know what they're going to hit you with next," she told Newshub.
"You actually are too scared to pick up your phone, come out of your house, because you don't know what is going to be the next email, the next phone call."
Back in December 2017, she was told her cows would need to be culled. Then MPI gave them the all clear.
Fifteen months later, there's been another change - the cows need to be slaughtered after all.
"We have made a mistake in terms of some of the animals we didn't identify early enough for slaughter," Geoff Gwynn, MPI's M bovis Programme Director, told Newshub.
"I've apologised for that, it was human error and I've apologised to them for that error."
Adding to Ferguson's anxiety is the way these pregnant cows were sent to slaughter.
She requested a same-day kill so her animals didn't have to languish in the concrete yard at the works overnight.
"It was the one thing I asked. Please, please. I begged them. Please make it a same-day cull and please make it close by."
But the animals ended up having to be trucked to Blenheim.
Ferguson says MPI assured her it would be a same-day kill. She followed the truck on the five-hour trip north to be sure - but soon learned the slaughter wouldn't happen until the morning.
Gwynn admits it shouldn't have happened.
"It's not met the promise we clearly made and that's not good enough from my perspective," he said.
The original response plan stated successful eradication would depend in part on "rapidly detecting new infected properties".
But farmers like Mark Stevenson say the tracing has been inaccurate.
His property got locked down over some suspect bulls - which he says never interacted with sick animals and MPI was aware it was a false trace.
"They were told that trace was not a trace. It doesn't exist," he told Newshub.
"It's pretty poor, it's bloody poor."
Duncan Barr says he gave MPI detailed information of other properties where infected animals had been sent from his farm. It's been four months and still no follow-up.
MPI says it is improving its processes, with Gwynn saying it's continuing to try and make it better.
"If I could have every trace visited within 24 hours I would, but that's not even possible."
Gwynn says mistakes have been made in "a number of areas" - but points out that eradicating the disease is something that's never been attempted.
A team of 30 extra staff are now on deck to help speed up tracing.