The company running the new National Animal Identification and Tracing scheme expects to recover $7 million in costs in its first year of operation, by levying farmers.
It expects the annual cost to drop below $6 million after that.
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.
The Government is funding the NAIT computer database and start-up costs.
But farmers will pay the on-going costs through levies.
NAIT chief executive Russell Burnard estimates it's going to cost cattle farmers about $2.45 per animal, through ear-tag and slaughter levies.
Cattle and deer owners have until 23 December to make submissions on the proposed levies and methods of collection.