The Ministry for Primary Industries says farmers failing to keep accurate stock movement records are hindering efforts to eradicate Mycoplasma bovis.
There are currently six properties with the cattle disease in the Wakanui area of Mid-Canterbury.
The National Animal Identification and Tracing scheme, or NAIT, helps track the movement of cattle and deer and is a vital tool in a disease outbreak response.
MPI director general Ray Smith said an increased focus on pushing NAIT has paid off this year, with higher compliance rates.
"One area we have taken more action is on NAIT compliance and that has yielded a result, we've gone from 60 percent to 96 percent compliance," he said.
"But we still have people, including people that get themselves tied up with M bovis, who are not recording the movement of their animals."
Smith said incomplete NAIT records has resulted in farms being placed under movement controls, which may not have been needed if animals were properly accounted for under the tracing system.
MPI's M bovis programme director Simon Andrew said most of the infected properties would be cleared by early next year and eradication remained on-track, but it was vital all farmers used NAIT properly.
"In our tracing work, we have identified some poor NAIT practices, which is disappointing," he said.
"Good NAIT records allow us to track any infection quickly, whereas poor records slows us down and heightens the risk that other farmers' cattle are exposed to M bovis.
"We've come a long way thanks to the hard work of farmers and the wider farming community and as we approach the end of another year, it's timely to encourage farmers to do the right thing."
Andrew said farmers should be aware that, where necessary, the eradication programme would refer those with poor NAIT records to MPI's compliance team for investigation.
MPI's national manager of animal welfare and NAIT compliance, Gray Harrison, said while NAIT use had improved, more work was needed.
"When a person in charge of animals fails their NAIT obligations, they potentially put the whole sector at risk," he said.
"There has been improvement with registering animals after they have been tagged, but I'm concerned there appears to be a belief that this obligation starts and finishes with the person who has animals born on the farm.
"Every person who has NAIT animals on their property, that were not born there, must ensure they are tagged, registered, and have had their movement recorded into the NAIT system.
"Not doing this could make you liable for an infringement or court prosecution if those animals remain unregistered, and, or, not recorded in a movement.
"We've had some serious cases before the court this year involving hundreds of unregistered animals, resulting in thousands of dollars in fines. The consequences might seem severe, but they're a drop in the ocean compared to what it would cost to this country if this disease - M bovis or something similar gained a foothold in New Zealand."
Harrison said anyone unsure about their NAIT obligations should contact MPI, as there was plenty of support and information available.