Activist group Animals Australia on Friday, August 7 made a complaint to the Federal Department of Agriculture, Water and Environment about the alleged breaches at two facilities.
The Australian Livestock Exporters’ Council is looking into what happened.
ALEC chief Mark Harvey-Sutton said the killings were distressing, unacceptable and inappropriate.
“Exporters have genuine care for the livestock in their supply chains, they act quickly to investigate, working closely with importers and in-market teams,” he said on August 11.
“The industry is regulated and there are systems in place to make any necessary decisions to stop future non-compliance.”
Mr Harvey-Sutton said offending facilities could be removed from supply chains if breaches were identified.
Animals Australia chief Glenys Oogjes says the system won't protect animals from brutal treatment until sanctions include licence suspensions.
“That Australian cattle in Indonesia are still being killed via the banned Mark I (restraining) boxes and roping slaughter should be of grave concern to all in the cattle industry,” she said.
“It was deeply disturbing that slaughter practices exposed in 2011 are still being used in 2020, despite the existence of the exporter supply chain assurance system.”
The Federal Government recently decided against appealing a Federal Court ruling that a six-month ban on live cattle exports to Indonesia, imposed by former Federal Agriculture Minister Joe Ludwig in 2011, was invalid.
Live cattle export-linked industries are expected to get hundreds of millions of dollars in compensation for the temporary ban.