The panel, which will be appointed shortly, is expected to report back in April next year.
The decision was made by the states' Primary Industries ministers in response to a recommendation which came out of the national equine flu summit held in Sydney on September 25, where proposals for an ongoing vaccination programme for racehorses were hotly debated.
Interest and industry groups attending the summit were divided on the merits and cost-effectiveness of such a programme.
The ministers, who met in Adelaide on Thursday, had gathered for the meeting of the Primary Industries Ministerial Council.
The ministers considered a range of issues affecting Australia's primary production sectors.