The company running the new National Animal Identification and Tracing scheme estimates it's going to cost cattle farmers about $2.50 per animal in levies to fund the scheme.
NAIT will take effect for cattle in July next year. Deer will be included from March 2013.
Cattle and deer farmers will be required to register their animals and fit them with radio frequency ear-tags to allow the identity and movement of livestock to be traced quickly and reliably.
The Government is funding the building of the NAIT database and some operational costs.
But farmers will pay the rest of the costs through levies.
They have a month to have their say on proposed levy levels and how they're collected.
NAIT chief executive Russell Burnard says a levy on ear tag sales is proposed for dairy and beef cattle and another when the animals are slaughtered.
He says a different cost-recovery system is proposed for the deer industry.
Farmers and others such as lifestyle block owners who manage cattle and deer have until 23 December to make submissions on the levy proposals.