More than a hundred animals are believed to have died on the sea in the incident over the weekend.
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Initial assumptions are that the cattle deaths on the live export vessel headed to Indonesia are a case of botulism.
Peak industry body the Australian Live Exporters Council said the affected animals came from a single property.
Efforts were underway to treat the remaining animals that may be affected, ALEC reported.
Botulism is a paralysing disease of animals, caused by a potent nerve toxin produced by the bacteria Clostridium botulinum.
Veterinarians have told ACM it would be entirely possible, even likely, the cattle were infected before leaving Australia. Symptoms can take some time to display.
Recent wet conditions in the Northern Territory may have played a role.
Government primary industry authorities report many cases of botulism are due to contamination of the feed or water by rotting organic matter containing the botulism toxin or bacteria.
High moisture feeds can provide an ideal anaerobic environment for botulism growth.
Much pastoral area in Australia also has phosphorus deficient soils. In these areas botulism occurs quite commonly as cattle chew bones and carrion containing botulism toxin to satisfy their craving for phosphorus and/or protein.
Due to the remote locations the affected animals may die unnoticed and only show up as reduced numbers at musters, government veterinary information says.
Cattle can be vaccinated for botulism. However, according to a Northern Territory government advice sheet, surveys have found that around 30 per cent of supposedly vaccinated animals in the Territory had no protection, with cattle missed at mustering a factor contributing to vaccination failure.
Concerns
Producers supplying the live export industry are already expressing extreme concern about misinformation around this situation on the back of a lack of general public understanding about botulism.
The vessel, the Brahman Express, is believed to have left Darwin on Sunday.
The Department of Agriculture, Fisheries and Forestry was informed of the deaths later that day by the exporter.
Prior to departure, all livestock loaded onto the vessel were assessed to be in good health and fit to load and were inspected by veterinarians, ALEC said.
The exporter has conducted itself correctly through the process and would work closely with DAFF to determine the cause of the deaths, a statement from ALEC said.
DAFF is also engaging with Indonesian officials to keep them informed of the issue.
"Australia is confident that there is no evidence of an exotic disease and that our Animal Health Status remains unchanged," ALEC said.
"Indonesia is Australia's most important trading partner for live cattle and it is important that we work closely and transparently with them as we work through this issue."