Farmers are not keen on an electronic identification scheme for all cattle and deer.
Federated Farmers says 80% of initial respondents to a survey of 14,000 members do not support the introduction of the National Animal Identification and Traceability Scheme.
It is due to become compulsory for cattle and deer by 2011.
NAIT Supporters say it will act as an insurance and help speed the resumption of trade in the event of an outbreak of serious animal diseases such as foot and mouth.
Federated Farmers argues that the programme will be costly to farmers, without providing them any benefits.
However, Silver Fern Farms (formerly known as PPCS) says the industry's view is that traceability systems need to be established now, in case there's a need to demonstrate birth to plate tracking in the future.
Chief executive Keith Cooper says having a system in place could help add value to the final product.