MPI's director of response Geoff Gwynne, speaking to RNZ about the Southland case this week, said fewer than 20 farms had had to be revisited since May 2018 when the eradication programme began.
However, in response to Herald inquiries, MPI said the actual number of farms that had been infected for a second time was five since May 2018. This was out of 1400 farms that had been under regulatory controls.
Of the five, four had been "depopulated", MPI's term for a cattle cull, and one was yet to be.
One was in Hawke's Bay, three in Canterbury (one here had still to be depopulated) and one in Otago. There were a total of 1900 animals across the five properties.
In October last year an independent technical group advising MPI reported it was confident the disease, which cannot be passed to humans through food, could be eradicated.
Asked if this opinion still held, MPI told the Herald "the programme - comprising MPI, DairyNZ and Beef+Lamb NZ - continues to be confident that eradication can be achieved and make sure that everyone can farm free from this disease in the future".
MPI said 214 farms had been confirmed to have M. bovis out of 24,000 farms across the country - 191 had been cleared.
The need to revisit and test a small number of farms was not a surprise, MPI said.
"Risk occurs when animals that are moved and not registered on the NAIT - National Animal Identification and Tracing - system, which records animals moving on and off farms.
"It's critical that all farmers continue to maintain up-to-date and accurate NAIT records."
Accurate record-keeping helped MPI track animal movements and locate any that could be affected, the ministry said.
Shortcomings in NAIT compliance by farmers have been highlighted since M. bovis was first identified in New Zealand in July 2017. But MPI said there was evidence compliance was increasing.
An MPI update says 232 properties are currently under a notice of direction, a legal direction restricting the movement of animals and risk goods off a farm, and 264 are under active surveillance where testing has started. Most are in the South Island, where the disease was first diagnosed. As at last month there were 23 active properties with M. bovis, all under quarantine.
M. bovis affects dairy and beef cattle and can cause mastitis, pneumonia, arthritis and late-term abortions.
The disease is endemic in the herds of New Zealand's trading partners. New Zealand is the first country to attempt to wipe it out.