More than 100 Australian cattle have died on a live export ship to Indonesia — likely one of the highest mortality rates ever reported on an Australian cattle shipment.

The Australian Department of Agriculture, Fisheries and Forestry has confirmed a number of cattle deaths were reported to the regulator over the weekend.

A department spokesperson would not confirm the exact number but said there was "no suggestion that exotic animal disease is involved" such as foot and mouth disease or lumpy skin disease.

The department said it was investigating the deaths from the vessel Brahman Express.

Under Australian regulations, an exporter must notify the government if a consignment's mortality rate is greater than 0.5 per cent or three head of cattle, within 12 hours.

"We have been notified by a commercial exporter of an incident involving cattle deaths on a live export vessel exporting to Indonesia," the spokesperson said.

"Australia remains free of exotic animal diseases such as Lumpy Skin Disease and Foot and Mouth Disease."

The cattle were likely shipped from Darwin and had been declared fit to travel by a government vet when loaded on the vessel.

Industry group the Australian Livestock Exporters' Council suggested botulism, a rare disease spread via bacteria, could be the cause for the cattle deaths.

"Initial assumptions are that this is a case of botulism, with the affected animals coming from a single property," ALEC chief executive Mark Harvey-Sutton said.

Mr Harvey-Sutton confirmed the livestock shipment was discharged in Indonesia on March 24.

"It does seem that there were some extraordinary circumstances that have seen this event take place. And obviously, we need to get to the bottom of why that has all occurred," he said.

"It was the exporter that self-reported this. They've been very clear and transparent about this issue all the way through, and they are working very closely with the Department of Agriculture."

He said he believed the cattle had come from a property in the Northern Territory.

"Australia is confident that there is no evidence of an exotic disease and that our Animal Health Status remains unchanged ... 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," he said.

Foot and mouth disease and lumpy skin disease, two livestock conditions potentially jeopardising billions of dollars of meat and dairy exports from Australia if detected here, were reported in Indonesia in 2022.

In 2011, the Gillard government announced a snap ban on live cattle exports to Indonesia by sea, a decision later found unlawful by the Federal Court.

The Albanese government has promised to ban live sheep exports by sea from Australia but is yet to set a date to end the trade.

Last year the value of cattle live exported from Australia was $1.2 billion, according to ABS data provided by LiveCorp.