Thousands of sheep stranded in Western Australia after the crew of an export ship contracted coronavirus will be sent to the Middle East, despite a shipping ban.

The future of the shipment of 56,000 sheep, worth an estimated $12 million, had hung in the balance, since docking in Fremantle in May.

The Federal Department of Agriculture this month refused to grant the Al Kuwait export ship an exemption to travel during the northern summer, shocking many in the WA livestock industry.

The trade ban period commenced on June 1, and is aimed at stopping sheep from overheating and dying on vessels.

It is understood the majority of the sheep can now travel on a different ship, which meets animal welfare requirements.

It is understood the ship must sail by Wednesday, and will carry about 45,000 of the sheep.

The future of the remaining sheep is unclear.

The sheep are currently being held in a licensed live export feedlot at Baldivis near Perth, and biosecurity regulations prevent the animals being sold back to farms.

-ABC