The Australian government affirmed on Friday allegations of animal cruelty that involved two Australian live animal exporters owing to their business connection with Indonesian abattoirs, which reportedly slaughtered animals using sub-standard techniques.

In a statement issued Friday, Agriculture Department Deputy Secretary Phillip Glyde identified the erring firms as International Livestock Exports and North Australian Cattle Company, which he said were determined as culpable for 37 counts of violations under the new animal welfare standards established in 2011.

Part of the breaches, the government report said, were the absence of effective head restrains prior to the actual killing of the animals and the lack of effective measures in confirming deaths before the cattle stocks were subjected to cleaning procedures.

"There were two Australian exporters who had breached the new export supply chain assurance system that was put in place by the Government last year," Mr Glyde was reported by ABC as saying on Friday.

Foremost of the firms' breaches were their failure to ensure that cattle coming from their stocks were treated humanely upon reaching their final destination in Indonesia.

"The action that the regulator has taken is to remove those two abattoirs from the supply chain of the two exporters," the agriculture official said.

The federal government launched its probe on the matter February 2012 when the animal welfare group, Animal Australia, called its attention on the alleged mishandling of Australian live animal exports to Indonesian abattoirs.

The group provided video clips to support its claims, with one scene, which was earlier broadcast by ABC, showing a local worker slitting the throat of a cattle, which was fully conscious at that time.

The group added that its probe on the incident also revealed the employment of an abattoir auditing system that it labelled as inherently flawed.

"This is not an auditing system that can be deemed independent and therefore relied upon," Animal Australia campaign director Lyn White said in a statement.

However, Mr Glyde said that the government's latest actions proved that it "does not tolerate the mistreatment of animals and takes all allegations of animal welfare abuse seriously."

He added that swift and definitive punishment awaits live animal exporters and "if further animal welfare breaches occur in these exporters supply chains, they face additional penalties under the relevant legislation, including the possible loss of their export licence."

As a direct result of its findings, the government said that two Indonesian abattoirs identified in the video clips will be blacklisted from conducting business with Australian exporters but another two have been cleared as the probe determined that they were not processing live stocks that came from Australia.

Mr Glyde also said that following the probe, the government now requires "those two exporters to have animal welfare officers present in all of their remaining abattoirs in their supply chain ... and to increase the intensity of (their) auditing."

The Agriculture Department also endorsed for the Chief Veterinary Office to conduct a review on the Mark 4 restraint boxes and determine whether its employment minus the mechanical head and neck restraints conforms to the guidelines released by the World Organisation for Animal Health.

In a separate statement, Agriculture Minister Joe Ludwig said that the incident and the ensuing government actions should convince the industry that "this new system provides the checks and balances the community expects for this trade."