Paul Watson, the captain of the conservation group's flagship the Steve Irwin, said the Brigitte Bardot had done its job in scouting out the location of Japanese whaling ships.
It would be available for its campaigns to protect sharks in the spring.
He said the small ship was adequate to handle the rough conditions of the Southern Ocean.
"Nothing is really appropriate down there," Captain Watson said.
"It is pretty hostile conditions.
"Any vessel can be hit by a rogue wave and this is what has happened."
The Steve Irwin was to leave Fremantle today to rejoin the Bob Barker, which is expected to take about seven days.