Three days later Watson — who was out on €250,000 ($320,000) bail in Germany pending a separate extradition request from Costa Rica — last reported to authorities.
Watson and his group have repeatedly clashed with fishing fleets they accuse of illegally hunting whales, sharks and other endangered sea animals.
Sea Shepherd said Thursday that the 61-year-old Canadian had left Germany and was now "in an undisclosed location."
Sven Matthiessen, a spokesman for the Sea Shepherd Conservation Society in Germany, said he didn't himself know Watson current whereabouts.
But he said the group had been aware of Japan's attempts to extradite Watson.
"There is some sort of connection between the requests made by Japan and Costa Rica," Matthiesen told the AP.
A spokeswoman for Germany's Foreign Ministry, where the Japanese request was filed, couldn't immediately comment on the case.
Watson was first arrested May 13 at Frankfurt Airport on a warrant from Costa Rica, which claimed he had endangered the crew of a fishing vessel a decade ago.
Sea Shepherd says Watson was filming a documentary at the time of the alleged incident, which took place in Guatemalan waters in 2002. The U.S.-based group said it encountered an illegal shark-finning operation run by a Costa Rican ship, the Varadero, 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 has a history of confrontations with whalers and fishermen.
He left Greenpeace in 1977 to set up the more action-oriented Sea Shepherd Conservation Society. The group has waged aggressive campaigns to protect whales, dolphins and other marine animals, prompting Japanese officials to labels its member terrorists.
Copyright 2012 The Associated Press.