After five-and-a-half weeks on board a livestock ship turned back from the Middle East, thousands of sheep and cattle have begun to be unloaded following the vessel's return to port.
About 16,000 animals have been packed aboard MV Bahijah since January 5, when it sailed from Fremantle before being ordered to abandon its voyage due to Houthi rebel attacks in the Red Sea.
Except for a couple of hundred head of cattle unloaded 10 days ago, the animals have remained on the vessel since it returned to Australian waters.
The lengthy delay sparked fears for their welfare as authorities considered a now-rejected application to send them on another even longer journey for export.
The Department of Agriculture, Fisheries and Forestry said the livestock would be taken on trucks to quarantine yards and held under strict biosecurity controls.
"Disembarkation is a complex process," it said on Monday.
"It is anticipated the discharge will take a number of days and all parties involved, including the department, WA government, exporter, transport companies and appropriate premises continue to work collaboratively to ensure the health and safety of the livestock and staff."
WA Farmers Livestock Council president Geoff Pearson said the livestock would be in the yards for at least 10 days to rest.
"Then (the exporter will) look at resubmitting a permit to export," he told AAP.
"They'll have to go through a whole new process as a new shipment."
The agriculture department last week refused an application to ship the livestock to Israel via the longer southern Africa route because export control rules had not been complied with.
It said it was not satisfied the animals' health and welfare could be assured on the journey.
Legal proceedings filed by animal activists in Israel in a bid to stop the ship from importing its cargo into the nation were also a factor in the department's decision.
A spokesman for Let the Animals Live and Animals Now told AAP the groups dropped the case after the Australian federal government rejected the application.
Australian animal advocacy groups have repeatedly raised concerns for the health and welfare of the animals due to the length of time they have been on the vessel and the extreme heat Perth has experienced in past weeks.
Authorities said 60 sheep and four head of cattle have died since they were loaded but this wasn't out of the ordinary given the total number of animals on the ship.
If the animals are re-exported they are likely to be at sea for a month as the Bahijah sails around Africa to avoid the Red Sea - an area where Houthi rebels in Yemen have targeted ships heading to Israeli ports.
