More than 30 livestock died on a ship while it was stranded in Perth for 10 days, but authorities still gave the vessel the all-clear to travel to South East Asia with the cattle.
The MV Ocean Outback was originally destined for Israel carrying 13,000 sheep and cattle, but encountered engine problems while departing Fremantle Port on December 29.
Ship owner Wellard Live Exports, which chartered the vessel to Otway Livestock Exports, confirmed the deaths of 30 sheep and three cattle on Sunday.
It said the remaining 5500 cattle were being shipped to South East Asia to be supplied to a regular accredited buyer, while the 7500 sheep were offloaded and transported to a pre-export quarantine feedlot.
When the vessel was in port, it was inspected by a veterinarian and animal welfare officer from the federal and state agriculture departments, and an RSPCA inspector before being given clearance to proceed.
In a statement, the federal department said there were no concerns for the welfare of the animals.
"They were found to be in excellent condition," the statement read.
"There were no injuries or mortalities during unloading and transport of the sheep to registered premises.
"All required biosecurity precautions were taken."
The cattle were also deemed fit for travel, with the exporter loading medicines, fodder and bedding materials in excess of what was normally required.
The department will continue to monitor the situation, but said the vessel complied with all AMSA requirements.
The RSPCA says it will continue to liaise with authorities about the welfare of the animals.
