Milk on all farms in North Otago and South Canterbury will be tested for the cattle disease mycoplasma bovis, the Ministry for Primary Industries says.
Plans have changed since two weeks ago when the ministry said it was going to test milk tankers across the country to try to determine whether the disease had spread.
Ministry incident controller Eve Pleydell said the ministry had a "fairly large" surveillance programme in place, and part of that would be taking bulk milk samples from all farms in North Otago and South Canterbury. Samples would also be taken of milk from cows infected with mastitis, which is usually discarded.
Ms Pleydell said instead of the tanker testing, the ministry was working with veterinarians across the country "to identify farms that have a health picture and a clinical picture that could be suggestive of this disease".
"We're working with 15 vet practices across New Zealand and we'll be identifying about 170 farms," she said.
The outbreak was first detected in late July, and so far the disease has been found on two of the 16 Van Leeuwen Dairy Group Farms in South Canterbury.
The highly contagious disease causes mastitis, pneumonia, abortions, lameness and death in cattle, which can also mean significant production losses for farmers.
The ministry said there was an international shortage of testing kits, but more were being manufactured from around the world. Tests need to be taken three or more times over three to four months before there was a definite result for each farm.
Ms Pleydell said it was estimated that, based on current knowledge, testing samples of milk, blood and swabs would take 12-13 weeks to complete.
"We're estimating that across all our different parts of surveillance we'll be having about 33,000 tests and samples that will need to be run.
"At the moment we have got about 4600 samples ... at the laboratory we've processed about 2068, so we've got a big job on our hands."
Since the disease outbreak there had been 13 calls to the ministry from across New Zealand about potential cases; 10 had been cleared and three were under investigation.
"So we still haven't had any positive cases come in through that route yet."
Ms Pleydell said if the investigation found the disease was contained to the two Van Leeuwen Dairy Group farms, the ministry would try to eradicate it.
But eradication would be far harder if it had already spread to other parts of the country. "It would be less likely to be the option."