The Filipino nationals are on their way to Melbourne, where they'll each fly back to their provinces.

The crew had arrived on the Chinese-owned, Liberian-flagged carrier Yangtze Fortune in September when a crack was found in the hull.

While a temporary concrete box was installed over the fault, the Australian Maritime Safety Authority had concerns about the longevity of the repairs and prohibited the vessel from loading cattle.

The ship was ordered to be sold off through closed tender by a federal court ruling after the vessel was deemed to be abandoned by the owner, which faced mounting debt.

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Harbour master Andrew Hays said while it wasn't uncommon for vessels to get "arrested", it was an unusual set of circumstances which came to a head.

"The period of time it went on for and the sale of the vessel is unusual," he said.

"Vessels will be arrested periodically for outstanding debts but they're generally paid so they can continue operating and earn money on the assets.

"It's really good to see the seafarers are going home after such a long period, it was a bad circumstance for them and it's great they're finally being repatriated."

Portland charity organisation Mission to Seafarers manager Neville Manson said the crew was "over the moon" to be leaving the "nightmare" situation.

"It's a great outcome, in Australia this doesn't happen very often," he said.

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