The confirmation, posted by Sea Shepherd executive Susan Hartland on the group’s website, comes hours after a German court issued an arrest warranty for Watson alleging he skipped bail.
Watson was arrested May 13 at Frankfurt Airport on a Costa Rican warrant that claimed he had endangered the crew of a fishing vessel a decade ago.
Watson was released days later on a $320,000 bond and ordered to report regularly to authorities while Costa Rica's extradition request was considered.
The Sea Shepherd Society maintains Watson's arrest was politically motivated.
Hartland says the group has ”reason to believe from a reliable source” that once in Costa Rica, Japan may try to extradite Watson to Japan to answer charges related to obstructing their whaling activities.
Hartland adds that the group has no further information and is not in touch with Watson.
Sea Shepherd says Watson was filming a documentary at the time of the alleged incident in Guatemalan waters in 2002.
The group says it encountered an illegal shark finning operation run by a Costa Rican ship and told the crew to stop and head to port to be prosecuted.
The crew accused Sea Shepherd of trying to kill them by ramming their ship.
Watson parted ways with Greenpeace in 1977 to set up the Sea Shepherd.
The group has waged aggressive campaigns to protect marine animals, prompting Japan to labels its members terrorists and to seek Watson's arrest for allegedly masterminding violent protests.