Foreign Minister Stephen Smith said a ship monitoring the whalers would retrieve the men as soon as possible.
The protesters, from radical anti-whaling group Sea Shepherd, boarded the Japanese ship on Tuesday.
Whalers say they want to return them, but Sea Shepherd says conditions for the release are unacceptable.
Mr Smith said that the patrol boat, the Oceanic Viking, would retrieve the men from the Yushin Maru 2 and transfer them to Sea Shepherd's Steve Irwin vessel.
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