Federated Farmers say farmers are being railroaded into accepting a compulsory animal traceability system.
The National Animal Identification and Traceability Scheme aims to introduce electronic ear tags for all cattle and deer by 2011.
It would also mean that individual animals could be traced back to the farm, and would aim to improve New Zealand's ability to respond to biosecurity alerts and to provide assurances on food safety to consumers.
NAIT says formal consultation has been completed and a roadshow is being planned to present farmers with the proposed scheme and to obtain feedback on how it can be fine-turned.
But Federated Farmers says that's moving too fast.
President Don Nicolson says the organisation's concerns are its concerns are not being heard despite being represented on the governance board of the organisation.
He says more analysis needs to be done before farmers are landed with a costly scheme that may not have significant benefits.
NAIT says the scheme is still only a proposal with details are still being worked out with all interested parties.