The Ocean Outback's engine failed on December 29 shortly after leaving Fremantle, Western Australia, carrying 7426 feeder sheep and 5614 feeder cattle.
Wellard Rural Exports, the ship's owner, said while three cattle and 30 sheep died, the department said the other stock were in excellent health.
The sheep were unloaded at Freemantle after inspection and biosecurity risks had been assessed as of no concern. The sheep were moved to registered premises and are required to be kept isolated from the national livestock herd.
The cattle remained on board to await export to South East Asia.
The department said the welfare of the livestock continued to be the highest priority when making decisions and the solution maintained the highest standards of animal welfare.
After the exporter loaded extra feed and bedding materials onto the ship, it left Fremantle again, on January 10.
