Cow disease Mycoplasma bovis could be in every region of the country, warns Agriculture Minister Damien O'Connor.
"There is not a region that is free from this, given the movement of animals which is part of the normal New Zealand farming system," O'Connor told the Herald.
The Ministry for Primary Industries (MPI) today said that the disease had been confirmed at a Waikato farm.
"It's the sad reality that there will be other farms come back as infected as we continually test properties that are identified as being at risk," O'Connor said.
Animals that had been moved to other regions, such as north of Auckland, were being tracked, he said.
"It is possible, and indeed likely, that they will come back as infected herds as those animals have spread the disease."
O'Connor said a decision would be made in the next two weeks on whether to halt slaughtering cows in a bid to eradicate the disease.
"It will be a decision we'll be making, with industry, as to what extent is it possible to contain and eradicate or indeed has it gone too far."
He said all infections so far had been linked back to the original infected properties.
"If we can identify all those movements, eventually we can wind that back. "
Tirau farmer and veterinarian Ian Scott said he would be disappointed if the Government moved towards a containment option and gave up on eradication.
"These animals that are now being identified as being positive ... as long as those farms have connections back to the original source properties then this is a normal part of a disease eradication process. From my point of view, I'd be disappointed if everyone throws their hands up in the air and says, 'It's all too hard'," Scott said.
Federated Farmers national dairy chairman Chris Lewis said most farmers "still want to eradicate it but the timeline has changed a little bit".
"To eradicate it we need a good plan in place and we also need the backing of MPI, but also the backing of the industry group to make this happen, and most importantly the backing of the farmers."
Prime Minister Jacinda Ardern told reporters the Government was trying to manage the issue.
"But I have to say, from all of the evidence I've seen, [it] seems to be a direct consequence of poor systems, processes and biosecurity investment. And we are having to now deal with that."
Ardern said she believed the full scale of the problem had not yet been seen.
"But we are working very closely with industry to make sure we have a full and adequate response."
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.
"It was, however, not a huge surprise given the sheer number of farms we are uncovering that have received cows and calves from affected farms," Gwyn said.
"It's a reality of New Zealand's farming system that large numbers of animals are sold and moved across big distances. This response is serving to underline just how much movement takes place and it is this, coupled with poor record-keeping through NAIT [national animal identification and tracing] that is making our job very challenging."
O'Connor has said changes will be made to the Nait system.
National MP Tim van der Molen said a lack of communication on the issue had left farmers feeling unsupported and fearful for the future.
"It is important for farmers across the Waikato region to be aware that it has reached our community, so they need to put precautions in place – I'd encourage them to contact MPI immediately for guidance on procedures and protocols."
The Waikato result takes the number of infected properties across the country to 39.
A cull of 22,000 cows is currently under way, with 11,000 animals already destroyed.
O'Connor said last week that farmers should ensure any compensation claims they made were accurate to speed up the process. MPI and Dairy NZ had boosted the number of people working directly with farmers to help.