The legislation setting up the framework for the levy passed in the lower house yesterday and is bound for the Senate.
The amount of the levy will be set only after any future disease incursions, in consultation with the horse industry.
The levy proposal was attacked by opposition MPs, who argued it was inequitable, with many unregistered horses unlikely to be subject to the levy. Opponents argued that the levy would place an unfair share of the responsibility on recreational horse owners.
The levy proposal is likely to go before a Senate committee.
The Australian Horse Industry Council said a decision to put the matter before a Senate committee would provide further opportunity for industry consultation on the merits of the current proposal.
But it added: "It might also further delay protection of the horse industry should there be an emergency disease outbreak while this examination process is under way."
The council said it hoped any senate review process would be completed quickly.
Without the levy, there is no guarantee of government assistance to the horse industry to respond to an emergency disease incursion, it said.
Agriculture Minister Tony Burke said the levy would bring the horse industry in line with other livestock industries protected under the Emergency Animal Disease Response Agreement (EADRA).
Mr Burke told parliament: "This is not easy policy by any stretch of the imagination.
"What we are dealing with here is something which has been worked through in all the other livestock sectors. Be it cattle, sheep, pigs or the chook market, all have levy systems in place.
"In each of those cases that was a much easier thing to set up because the common point is that these animals are being raised for slaughter. So it makes sense to impose a levy and it is very easy to find the point where you would impose a levy.
"The worst option of all would be for the horse industry not to become part of the Emergency Animal Disease Response Agreement.
"The members of those three peak [horse industry] bodies are not unanimously in support. Of course that is the case; you never get wild enthusiasm when a levy is involved.
"But we have to make sure that the sector is protected into the future. We also need to understand equine influenza is not the only threat here."
"Because so many people - whether they are involved in pony clubs, harness racing or general racing at the track - have been through a terrible time with EI, that has, understandably, characterised much of the debate, but we have to remember that this legislation is about protecting the industry if there is another outbreak of something.
"Looking to the future, this package of bills will give the horse sector the certainty that other livestock sectors have when responding with government to emergency animal disease incursions.
"These bills will enable the horse sector to become a party to the EADRA, the Emergency Animal Disease Response Agreement - something that they have wanted for years and have been right to want.
"In short, this package of bills provides certainty for resourcing emergency responses to future horse disease outbreaks."