The Exporter Supply Chain Assurance Scheme was established in 2013 following revelations of horrific cruelty in Indonesian slaughterhouses. The revelations prompted the then Labor Government to suspend exports to the country.
The system is supposed to ensure that Australian animals remain within approved supply chains. But in March, the live export industry itself reported that thousands of cattle in Vietnam had been killed outside the system.
The Australian Livestock Exporters' Council also reported three welfare breaches including the use of sledgehammers to stun or slaughter, which the Department of Agriculture says it is still investigating.
A spokesman for Agriculture Minister Barnaby Joyce said officials were seeking to ascertain whether the Animals Australia footage related to one of those incidents, or a new breach.
Dismissing calls to halt exports to Vietnam, the spokesman said the Government remained "totally committed to the live export trade", adding: "When problems arise, we deal with the specific problems, we don't shut down an entire industry."
The Prime Minister, Tony Abbott, said the suspension of exports in 2013 was a "catastrophic decision" which "cost thousands of Australians their livelihoods ... [and] badly damaged our relations with Indonesia".
The industry denounced the "cruel and outdated practice of stunning by sledgehammer", saying that the cattle in the footage had been "illegally removed from our supply chains for quick buck processing in non-approved slaughterhouses".