The Australian Department of Agriculture, Fisheries and Forestry confirmed several cattle died on the Brahman Express over the weekend, but would not confirm the exact number.
Efforts are underway to treat remaining animals that may be affected.
Mark Harvey-Sutton from the Australian Livestock Exporters Council said botulism - a rare poisoning that attacks the nervous system - was likely to blame for the more than 100 deaths.
"Based on evidence so far we believe the cause of the death is botulism, but we are awaiting confirmation from the department of agriculture," Mr Harvey-Sutton told AAP.
The exporter reported the deaths to the department as soon as the deaths were discovered, he said.
"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 agriculture department said it was investigating the deaths as a "matter of priority" and there was no suggestion an exotic animal disease was involved.
"Australia remains free of exotic animal diseases such as lumpy skin disease and foot and mouth disease," the department said in a statement.
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.
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