Biosecurity New Zealand's response director Geoff Gwyn said it was disappointing to find the disease in another of New Zealand's key dairying regions.
"This is something we are trying to manage as a new government, but I have to say from all of the evidence I have seen, it seems to be a direct outcome of poor systems, processes, and biosecurity investment and we are having to now deal with that", Ardern said.
Ms Ardern said from her perspective the government were having to "pick up the pieces of significant neglect and under-investment, and quite frankly from what I've seen it's shameful".
It is the first time a farm in Waikato had tested positive for the disease. The infected farm was identified through the tracing of cattle movements from other infected properties.
Since the beginning of the response, Biosecurity New Zealand (MPI), animal industry bodies, vets and farmers have been intent on identifying new infected farms, containing the disease and keeping all options open to make the best possible decision on how the disease should be managed in future.
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Federated Farmers national dairy chairman Chris Lewis said most farmers "still want to eradicate it but the timeline has changed a little bit".
"That amount of movement, this can not surprise anyone in the Waikato".
The disease was detected last Wednesday on a mixed sheep and beef farm in north Canterbury - the first confirmed case in the region.
"It's here now, you have to look after your own farm and protect it".
"The next couple of weeks is going to push the limitations of restricted place notices or farmers making sure they do their job properly".
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He urged farmers to take care and communicate with their transport operators or graziers when moving cattle to prevent the disease from spreading and follow the rules around Nait.
"The signals that have gone to them from the Government when they introduced NAIT and then never enforced it have been pretty soft", Mr O'Connor admitted.
"It is possible, and indeed likely, that they will come back as infected herds as those animals have spread the disease".
National Party MP for Waikato Tim van de Molen said his thoughts were with the affected farmer.
"I acknowledge that this is a hard and challenging time for all involved but the government and MPI needs to maintain open communication with affected stakeholders and this is now not happening".
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"However, he - like so many others - is frustrated with what he feels is a lack of communication and action from MPI".