About 80 sheep have died while being air freighted from Australia to Indonesia.
The Australian Livestock Exporters Council said the breeder sheep deaths occurred on Saturday evening and it characterised the incident as regrettable.
The sheep were headed to Jakarta.
The federal agriculture department, which is the industry regulator, has received an immediate report.
The council, LiveAir, the exporter and the air freight operator will work with the regulator as the investigation progresses.
Live sheep exports by sea will be banned from May 2028 after legislation passed the Senate in July.
Labor vowed to end the trade following animal rights concerns after thousands of sheep died of heat stress while en route to the Middle East.
The RSPCA has long campaigned against live exports and says the industry is “unfixable”.
The federal government has slated a $107 million transition package to flow to affected farmers.
Last-minute lobbying by West Australian farmers and exporters was not enough to have the legislation blocked.
Farmers have warned that some WA towns will die once the law comes into force and vowed to target Labor’s marginal seats.