A new electronic animal tracking system aimed at boosting biosecurity responses is gearing up to start in six months and will eventually monitor about nine million cattle, but farmers are concerned about the cost.

The National Animal Identification and Tracing (Nait) scheme will create an electronic database and is planned to start for cattle on November 1, depending on legislation, with deer to follow in March 2013.

The scheme will use radio frequency identification ear tags to track cattle from birth, through farms, saleyards and to processors.

Nait chief executive Russell Burnard said the current tagging schemes used a manual paper process to track back in the event of a biosecurity outbreak.

The Waiheke Island foot and mouth hoax in 2005 was a wake-up call for the country, Burnard said.

Nait said it took MAF two weeks to be satisfied with the identification of all at-risk animals in the Waiheke scare. Under the new system it would have taken 48 hours.

Any cattle moved from a farm after November 1 will be tagged with a Nait tag and any cattle born after that date will be tagged within 180 days and other stock within three years.

Burnard said there had been a mixed response to the scheme beween farmers who felt Nait should have happened long ago, those who just wanted to know the rules and some who were antagonistic.

"I think we've got more in the former two than we have in the latter category but there will always be some who say it shouldn't happen."

The Crown would provide, at most, $7 million to establish the scheme, plus 35 per cent of ongoing operating costs, with 65 per cent funded through levies.

Ongoing operating expenditure would be about $6 million a year and Nait was working through the levies with its owners - DairyNZ, Beef and Lamb, and Deer Industry New Zealand, plus regulatory body the Ministry of Agriculture and Forestry.

"We're close to coming to what that final cost will be ... but it's likely to be a mix of tag levies and slaughter levies," Burnard said.

Federated Farmers president Don Nicolson said there was a lot of consternation about the new system and how it would add benefit over cost.

"They said [the current system] wasn't good enough, based on Waiheke. Well I think that's a poor example," Nicolson said.

"I'd love to know where it's broken down on the mainland."

Beef and Lamb New Zealand chairman Mike Petersen said: "This is about future-proofing the industry, because if you can't demonstrate to your trading partners that you've got an effective traceability system in place then you won't be allowed to resume trade."

Farmers spoken to by Beef and Lamb were by and large accepting of the system, Petersen said.

"There's no doubt they have concerns about the cost of it and the time that it will take, they justaccept that unfortunately it's a price to pay now for getting access to the markets."