The industry, including farmers, lifestyle block owners and farming support services are said to have failed to record cattle movements in the system because its design has made the job onerous.
This failure has contributed to officials' difficulties in tracing potentially infected cattle.
The Government this month announced work had started to improve NAIT.
An MPI spokesperson said if farmers followed sensible precautions any risk could be greatly minimised.
"Preventing animals from moving would likely result in very challenging animal welfare problems for many herds prevented from moving, through lack of feed and degradation of pasture over winter.
"All farms that are infected or high risk are under movement controls so will not be moving stock.
"Farmers should have confidence in dealing with farms that are not under regulatory controls, so long as they are carrying out good biosecurity measures including NAIT compliance, understanding herd health history, and using good on-farm biosecurity measures."