New passport rule
Animal passports are set to be withheld from farmers until they provide evidence of a completed BVD test for every new-born calf.
The measure is included in the first draft of the legislation designed to make BVD a notifiable disease for the start of the compulsory phase of the programme at the beginning of 2013.
More than 378,000 samples have been analysed through the voluntary phase so far, with a 0.6pc BVD virus positive rate.
AHI is also finalising the criteria that will allow the year spent voluntarily participating in the BVD count as one of the three compulsory years.
"There are a number of 'red-line' issues which will probably disqualify a farmer from using the voluntary phase of the programme as one of the three mandatory years," said Mr Flaherty.
"An example of a red-line issue would be if we had evidence that a farmer sold on an animal after receiving a positive test result for it.
"But there could be mitigating circumstances and 90pc of farmers were fully compliant."