Federated Farmers says unease is growing among farmers over the National Animal Identification and Tracing scheme.
The scheme, currently undergoing public consultation, will be introduced on farms next year and made compulsory by 2011.
It will initially cover cattle and deer, with the aim of including other livestock species later.
Federated Farmers questions the cost benefits of a scheme that requires elecronic ear tagging of stock.
It is also concerned about other potential uses of the Government-run data system, FarmsOnLine, which will be used to collect and store the information from the livestock identification scheme.
National president Don Nicholson says Federated Farmers considers New Zealand is meeting its international trade and disease control obligations with existing traceability systems.
He says it's seeking the answers to nine questions it's raised with the NAIT planning group, covering its concerns.