About 16,500 livestock have been packed aboard the MV Bahijah since January 5, when it sailed for the Middle East from Fremantle before being ordered to abandon its voyage due to Houthis' rebel attacks in the Red Sea.
They have remained on the vessel since it returned to Australian waters, sparking fears for the welfare of the animals as authorities consider an application to send them on another even longer journey for export.
The ship docked in Fremantle Port on Friday, according to The Department of Agriculture, Fisheries and Forestry, after briefly berthing on Thursday.
The department said it was taking on provisions, including fodder and fuel, and the exporter's veterinarian was on board to monitor the animals' health and welfare.
"There should be no doubt Australia's biosecurity and the health and welfare of the livestock aboard are our highest priorities," Secretary Adam Fennessy told reporters at a brief press conference.
He said the agency would consider export laws, the animals' health and the length of time they had already been at sea, and Australia's obligations to its trading partners as part of its assessment to re-export the animals.
"It is a complex process and this is a unique situation," he said.
On Wednesday, the federal government sent two veterinarians onto the vessel to inspect the animals.
Australia's Chief Veterinary Officer Beth Cookson said there were no significant animal health or welfare issues or signs of exotic disease in the livestock.
If the animals are re-exported they're likely to be at sea for another month as the MV Bahijah sails around Africa to access Jordan via the Suez Canal and avoid the Middle East conflict zone.
Animal rights groups Let the Animals Live and Animals Now have meanwhile reportedly filed legal proceedings in Israel's Central Region District Court against the nation's agriculture ministry in a bid to stop the ship exporting its cargo into Israel.
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