Prosecutions have been launched against farmers who have failed to track their animals since the 2017 mycoplasma bovis outbreak.
Many farmers undermined New Zealand's biosecurity by not recording when and where they move their cattle.
"If they don't record them it makes it really difficult to try and track and prevent the spread of a disease," said Kevin Forward, head of National Animal Identification and tracing (NAIT).
The Ministry for Primary Industries (MPI) have launched three prosecutions against farmers for breaking the rules.
"Those that aren't following the law do need to be chased up and prosecuted. Any system that doesn't have some form of enforcement is going to be problematic," said David Acland from Federated Farmers.
MPI has also handed out more than 800 fines to farmers since the mycoplasma bovis outbreak began.
"Those who are complying are getting a bit sick and tired of those who aren't and they're putting at risk the livlihoods of themselves, their neighbours and the whole industry," said Mr Forward.
Two hunder and twenty properties have been infected by the disease so far and 130,000 animals have been culled.
'If you're only using the system once a year, it's a clunky system, it's very difficult, especially for some of the older generation within farming," said Mr Acland.
"Federated farmers at the begining ran a vociferous and in my view pointlesss campaign against NAIT and it really ruined its adoption by farmers from the get go," said agricultural economist Peter Fraser.
Farmers have been paid $123 million in compensation.