The bills were rejected by Opposition coalition senators last week in a move which Agriculture Minister Tony Burke said left Australian racing and recreational horse owners shouldering a major financial liability in the event of a major equine disease outbreak.
The legislation was drafted to provide a mechanism allowing the government to recover the cost of containment and eradication from horse owners through a levy.
"The Opposition showed reckless opportunism in voting against this Bill - and ignoring the agreement of peak industry groups," Burke said.
However, the Opposition rejected the criticism, saying that while the bills were well-intentioned, they were rejected them in the interests of ensuring that any such future levy can be applied fairly to the Australia horse community.
The bills sought to create a mechanism whereby a levy would be collected from horse owners at the initial registration of a foal or horse with a breed organisation.
"The coalition supports cost-recovery measures generally and we support the principle of introducing a levy mechanism to help cover any future costs associated with horse disease outbreaks in Australia," said Richard Colbedk, shadow parliamentary secretary for agriculture, fisheries and forestry.
"But we could not support the legislation put forward by the Government because it would have resulted in a small group of horse owners and breeders propping up the entire industry in the event of a disease outbreak.
"This would be completely unfair.
"In some cases, owners of the horses which expose Australia to the greatest risk of introducing diseases would not be required to make any levy contribution, but meanwhile backyard hobby breeders would be footing the bill.
"The collection base proposed was just not fair."
Colbeck said the government must go back to the drawing board.
"The mechanisms proposed in this legislation were drastically flawed and showed no understanding of the Australian horse industry and horse owners," he said.