Nearly 4000 sheep and more than 500 cattle died while being shipped overseas in the first half of 2017, with one particularly deadly voyage under investigation.
The figures were published in a report to federal parliament, tabled on Thursday.
Almost 777,000 sheep were loaded in Australia for export between last December and June this year, and almost 445,000 cattle.
About 0.5 per cent of the sheep (3839) were lost, and 0.12 per cent (522) of cattle loaded.
Almost 100 cattle died on a ship carrying 1236 en route to Malaysia and Brunei on an eight-day trip from Darwin in April. Ninety were euthanised as a result of slipping.
It was the first voyage of a new livestock vessel, which has already had its Australian certificate revoked.
It can't be used for export again until it has a valid certificate.
The Department of Agriculture and Water Resources and the Australian Maritime Safety Authority are investigating the incident.
"The mortality rate for this consignment was 7.79%, exceeding the reportable level of 0.5% for voyages less than 10 days," the report said.