Two new properties in South Canterbury are in lock down because of the cattle disease mycoplasma bovis.
However, the farms have not tested positive for the disease, but the ministry said the test results from one of the farms was "suspicious".
About 4000 cows are being culled, all from Van Leeuwen farms.
The slaughter has been backed by the the farming sector as well as the owner, Aad Van Leeuwen.
The disease can cause lameness, mastitis and abortions in cows, but poses no risk to people.
The new farms under quarantine are both owned by the same person, and border infected Van Leeuwen Group farms.
Geoff Gwyn from the Ministry for Primary Industries said as a precaution it put restricted place notices on both the properties, and expected a confirmed test result by the end of the week.