The Australian Department of Agriculture, Fisheries and Forestry confirmed several cattle died on the Brahman Express over the weekend of March 23 and 24, but would not confirm the exact number.
The department says it is continuing to investigate the cause of the deaths. Clinical signs present in the cattle are consistent with botulism.
Botulism in cattle is most often caused by the cattle eating a toxin produced by bacteria in contaminated feed. It is not a contagious or exotic disease and is not a risk to the Australian herd or to human health.
The department said detecting botulism through tests is often difficult, owing to the low amounts of toxin present in the bloodstream of affected cattle.
“As a result, testing for botulism is a process of elimination and will take some time,” a department statement said.
“Testing undertaken at the Northern Territory Government’s Berrimah Veterinary Laboratory has excluded bovine ephemeral fever and tick fever as possible causes of mortality. A number of other tests are still under way as part of the investigation.
“Australia is confident that there is no evidence of an exotic disease, and our animal health status remains unchanged.
“The department is committed to working closely with our international trading partners to provide assurance that all animals exported from Australia comply with their animal health requirements.”
Mark Harvey-Sutton from the Australian Livestock Exporters Council said the exporter reported the deaths to the department as soon as they were discovered.
"The exporter has gone through the proper process here, including when loading the cattle and exporting the consignment," Mr Harvey-Sutton said.
"Botulism is a disease that can be found in soil or pastures and symptoms can take some time to show, and it's entirely possible that these deaths could have happened on land."
The affected animals were believed to have come from a single property in the Northern Territory.
The cattle were inspected as required under the Export Control Act before leaving Darwin on March 14. The ship arrived in Indonesia on March 20.
