She said hearing the cattle disease was in the Waikato was "another blow around management of this issue".
Ardern said she had wanted to hear first hand from industry and farmers about the likely impact the disease would have on their lives.
Over the next seven days, a decision would be made about the next steps in the fight against the disease, based on technical advice and feedback from industry.
"Of course, we continue to pursue eradication but we also need to hear from industry and farmers themselves what their hopes are."
Ardern said the $85 million allocated to Mycoplasma bovis in the Budget was specifically for culling cattle.
"But that is a starting point. We fully acknowledge in the wake of the Budget this could cost New Zealand much, much more."
Asked at what point New Zealand had to accept the disease was here to stay, Ardern said the time was "not yet".
"We can learn from other countries' success and failure, but we need to come up with a plan that is unique to New Zealand."
Ardern said it was thought 38 farms in New Zealand were infected with the disease, with potentially 70 farms overall.
She said her meeting with Waikato farmers was a "conversation".
"Lots of exchanging of information and getting feedback around what they wanted to see from us. As much certainty as possible was the obvious message.
"But there's still a mixture of views out there so we are trying to make sure we have all this, and taking on board the technical advice, so we can make a decision no-one regrets."
Ardern said she had been discussing the pace of MPI compensation for affected farmers with O'Connor.
"We do know that is part of the certainty - we don't want farmers to be on a knife edge at this really stressful time. We'll keep working with MPI to see if we can speed things up."
O'Connor said the disease "may have been underestimated in the beginning".
"In hindsight perhaps mistakes may have been made. In the end, this is a unique challenge and we are doing the very best we can."
He said the police had assisted the Ministry for Primary Industries to "obtain information" during the ministry's ongoing investigation into how the disease entered New Zealand.
Progress on this investigation was expected in the "next month or so".
Mycoplasma bovis, first diagnosed in New Zealand last year in the South island, is a bacterial disease with multiple symptoms including painful mastitis and arthritis. It is not a danger to humans and does not affect milk and meat. It is established in the herds of New Zealand's trading partners.
A Government investigation has been underway for months as to how it entered New Zealand, which until last year along with Norway were the only countries not to have the disease.