"We are mindful of the impact cash flow has on business," he said. It's a process we've streamlined as fast as possible - the reality is we still have situations where farmers are feeling as though they're not being compensated but in reality they're not putting in a claim at this point. It's pretty hard to process a claim that hasn't been submitted."
Mycoplasma bovis was first confirmed in July on two farms in South Canterbury, marking New Zealand's first official outbreak of a disease that is present in many other countries.
While the disease presents no food safety risk, it can cause a range of symptoms in cattle including mastitis that doesn't respond to treatment, pneumonia, arthritis and late-term abortions.
Read more: Mycoplasma bovis total rises to 24
Director-general Martyn Dunne told politicians the ministry is still optimistic it can eradicate the disease, but that a final decision will be made this month.
"Our aim is to eradicate. We're not going to say we're going to long-term management now - our aspirations are to remove this if we can from the New Zealand herd," he said.
MPI has gone back to the government for funding the response where it's needed to, and Dunne said he's "confident" it will be considered in the upcoming budget requests.
Dunne said the ministry is negotiating with industry on its financial contribution to the outbreak, and said he would prefer cost recovery being through a government industry agreement rather than outside that process.