Federal Agriculture Minister Tony Burke spelt out the government's position in a letter to Australian Horse Industry Council (AHIC) president Barry Smyth.
The minister urged the horse industry to sign up to the Emergency Animal Disease Response Agreement (EADRA), which would involve horse owners paying a levy.
Burke wrote to Smyth to formally tell the council of the government's decision not to charge horse owners for the $A100 million eradication effort for equine influenza.
Burke had indicated publicly last week that the industry would not be asked to pay, saying it would not be proper to legislate retrospectively to recover costs for the outbreak, and that the industry should not be expected to pay for "the former government's failures".
However, in his letter, the minister said: "I must emphasize that the circumstances surrounding this emergency response are unique and this decision should not be considered as setting a precedent of any kind.
"No future assistance for emergencies will be provided until the horse industry becomes a full signatory to the EADRA."
He continued: "I would be most concerned if a future response to an emergency horse disease was jeopardised because the industry had not signed EADRA."
AHIC's Smith said the minister's letter makes it perfectly clear that any future government assistance for emergency diseases in the horse industry are entirely dependent on the horse industry becoming a signatory to EADRA.
"Without this contractual assurance of government assistance to mount an emergency response to a disease incursion, the industry will be left on its own - and the implications of that are all too obvious for the future of the industry."