A statement from the Fish, Food and Allied Workers-Unifor union says eight Ukrainian and three Russian crew members on board the Jana have been paid.
Gerard Bradbury with the International Transport Workers Federation says six of the men will fly home on Thursday.
Some of the crew have chosen to stay on the vessel and work for the new owners.
Donations poured in after Bradbury held a news conference last month as the men ran low on water and food.
He said at the time that the crew were owed about US$160,000 in total after the ship's former owners filed for bankruptcy in Germany.