Mycoplasma bovis has been found on a farm in Selwyn, just months after the country reached no known cases of the cattle disease.
A standard bulk tank-milk background screening picked up the infection.
The Ministry for Primary Industries (MPI) will work with the farmer to clear the farm of cattle.
MPI is tracing animal movements to identify the likely source of the infection.
“The find is unsurprising as we expected to identify more infected properties during spring testing, and it does not undermine our progress toward eradication,” MPI said in an update.