The anti-whaling organisation Sea Shepherd claims three men from the group Forest Rescue boarded the Japanese vessel Shonan Maru 2 in the middle of the night in waters off Bunbury in WA's south west.
It says the protestors went on board carrying the message "Return us to shore in Australia and then remove yourself from our waters."
It claims they are now being held on board the Shonan Maru 2.
Sea Shepherd says the Japanese boat had been tailing its flagship vessel the Steve Irwin while it towed another of the society's boats, the Brigitte Bardot, to safety in Fremantle.
The Brigitte Bardot was damaged by a 10 metre wave in the Southern Ocean.
Michael Montgomery from Forest Rescue says the men took boarded the vessel because the Federal Government is not doing enough to prevent the killing of whales.
"So it's up to the people to stand up and reclaim our personal power and stand up for what's right," he said.
The Federal Government is yet to comment.