Tony Burke outlined his position in a letter to Dr Roger Lavelle, president of the Australian Horse Industry Council.
Burke's letter was written after a recent meeting of state agriculture ministers in Darwin, where it was decided the horse industry had until December to come up with a levy deal or face vaccination.
A voluntary vaccination programme is backed by thoroughbred interests, who believe it would help the industry bounce back quicker in the event of any future flu incursions.
However, such a programme would make it harder to identify and control any future outbreaks because vaccinated horses can still get infected, but show few or no symptoms.
Voluntary vaccination would almost certainly result in the need for five weeks of quarantine for horses coming from Australia to New Zealand.
Burke, in his letter, said: "The Australian Government position on EI response options is that, unless the horse industry becomes a party to the Emergency Animal Disease Response Agreement, it will be unable to underwrite the costs of a response to an emergency horse disease event.
"As long as this is the situation, the government considers that the horse industry sectors should have the option to use a vaccine to mitigate the risk of EI to individual horses.
"The Australian Chief Veterinary Officer has spoken in support of this positon.
"I note that the council is continuing to work to secure the support of its membership in becoming a signatory to EADRA and, as a pre-condition, putting in place horse industry levy arrangements."