No farmers have been caught out yet at the Ministry for Primary Industries stock truck checkpoint in Picton, it says.
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The outbreak of mycoplasma bovis has highlighted that the National Animal Identification and Tracing system, NAIT, is not working.
In an effort to crack down on farmers who aren't using NAIT, the ministry started 'Operation Cook Strait' on Friday.
Some farmers haven't kept official NAIT records of stock movements, and it's slowed down the tracing of the disease spread.
MPI's manager Compliance Investigation, Gary Orr, said there's been eight trucks checked so far.
"Pleasingly there has been no problems at all so far. All the documentation has been present on the trucks and all the animals are compliant."
He said the checkpoint isn't taking long.
"We've been very careful to make sure there is minimum disruption to the drivers, we speak to them at the ferry terminals in Picton.
"We've had fantastic co-operation from the drivers and from the two ferry companies.. it's gone very very smoothly"
If animals aren't tagged then MPI doesn't have the power to keep the cattle in the South Island.
"There's no power under the Act to turn that animal around, but what we would then do is follow up enquiries with the farmer that had sent the animals."
"There are exceptions within the legislation for those animals that are difficult to tag... but they'd have to prove that to us."
If MPI isn't satisfied, then it will be fining farmers, he said.
The decision to check cattle crossing the Cook Strait comes eight months after the disease outbreak, but Mr Orr said it has taken time to understand the 'disappointing' level of NAIT non-compliance.
"We then had to try and find resource from within an existing resource, to try and do something about it.
"We've started off by having a look at stock movements between the South and North Islands... and we'll assess that in the next week or so and then determine how more widespread it should go."