The Ministry of Primary Industries has admitted its response to the Mycoplasma bovis outbreak could have been better communicated to farmers.
"Every day you learn more," MPI director Geoff Gwyn told The AM Show.
"So if you're to say, did we make mistakes earlier on? Hindsight's a wonderful thing and maybe we did."
On Monday the Government opted for an eradication approach to tackle the cattle disease, announcing a further 126,000 cows will be culled on top of the current 22,000.
But the response by MPI, which has been communicating the Government's response effort to the public, has been slammed by farmers on the front line.
"To put it politely MPI has been challenged," principal consultant at Agrifood Systems Keith Woodford told The AM Show.
"They didn't have the systems in place. They still don't have the systems in place."
Mr Woodford says once MPI accepts that, "we have a real chance at moving forward".
"It's a disease that until now there has been very little information about. No other country that I know of even records the incidents so it's totally left to farmers to manage.
"They have been caught out quite badly... What we now have to focus on is maximising the chances that it will work out."
Mr Gwyn says he respects Mr Woodford's views and admits there are "always things you can do better".
"My view is we're doing okay. We've learned lessons along the way. The reality is, and this is the same for all biosecurity responses, you're acting with limited information and you're making the best judgement calls you can, supported by international science.
"I think we've done the right thing in terms of tracking down the distribution of the disease... We have one shot at eradication and we're going to give it a go."
Communication has been "challenging", Mr Gwyn says, but noted MPI has had 60 public meetings attended by 16,000 farmers, sent out "thousands of letters" and set up websites and subscription emails.
"It's always hard when you're trying to communicate with a larger audience."
Mr Gwyn also acknowledged in some instances, "compensation has been too slow".
"There are some people out there very happy with the compensation process. But again those people tend to not talk to the media."
Prime Minister Jacinda Ardern told The AM Show an extra 250 staff have been employed to support MPI.
"We haven't seen something like this before. That does mean some errors have been made. It has not been flawless.
"But yes I have to have confidence in them, we're relying on them to help us eradicate this. We have to resource them to do it."
Ms Ardern says in terms of a "national impact", we're "no worse off for trying" to eradicate the disease.
"But for those 1 percent [of farms affected by M bovis], this is a big ask, I acknowledge that. They will be fully compensated and that's what we need to make sure we're really focused on."
Ms Ardern asks farmers whose stock has been cleared to take part in Gypsy Day to still "take precautions".