Being able to trace animals from birth to processing meant New Zealand could enhance its international reputation for producing high-quality food.
"In the case of a biosecurity outbreak affecting livestock, Nait will enable a quick and efficient response reducing the impact on the agriculture sector and the entire New Zealand economy," Carter said.
It was also an opportunity for farmers to increase productivity by identifying superior animals, he said.
First proposed eight years ago, Nait will require farmers to keep records of each animal's movements, whether off or onto the farm.
Records of all deaths, losses or exports of live cattle or deer must also be kept.
While the move has been accepted by most industry bodies, it has met stiff opposition from Federated Farmers.
Anders Crofoot, Federated Farmers Board spokesperson on national identification and tracing, said the group opposed a mandatory scheme.
"Our position has been that it would be much better as a voluntary regime. That would be as easy and cost-effective to implement."
Crofoot said Federated Farmers has accepted Nait is going live and the group is aiming now to make the roll-out as easy as possible for farmers.
One of its main concerns has been the cost, with farmers having to pay about $2 or $3 more for Nait-compliant ear tags than for the current non-electronic tags.
Other concerns were with what some considered obsolete technology, the powers the overseeing organisation would have, and the prospect that information gathered would be used to calculate charges for farm animals' greenhouse gas emissions.
Crofoot has been appointed to chair the Stakeholder Council that will oversee the merger between the Animal Health Board (AHB) and NAIT.
The Animal Health Board's role is to control bovine tuberculosis in cattle and deers and, like Nait, keeps record of livestock movements.
The Nait scheme already has about 30,000 people and their properties registered on the database, which will store information about each animal's RFID number, location, and the contact details of the person in charge of the animal.
It is very hard to know exactly how many people will need to register, but the law covered anyone with cattle or deer, regardless of the number, Crofoot said.
"If you've got a pet cow, that has to be registered."
The RFID can transmit only up to about a metre and farmers will scan the tags using a wand-like device or panel reader.
Crofoot said the first point of enforcement will be at the meatworks but animals will also be checked at the saleyards.
Government and industry are sharing the costs of operating the NAIT scheme.
