Paul Watson was arrested at Frankfurt Airport in May on a Costa Rican warrant that claimed he had endangered the crew of a fishing vessel a decade ago.
The environmental activist was released days later on a $320,000 bond and ordered to report regularly to German authorities while Costa Rica's extradition request was considered.
He went missing in late July and Sea Shepherd confirmed he had left Germany, though the group said it had no further information on his location and was not in touch with him.
Interpol says the information it received from Costa Rica prompted it to ask its 190 members to arrest Watson so the extradition process can resume.
The Sea Shepherd Society maintains Watson's arrest was politically motivated.
The organization 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 Society.
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.
Japanese officials have said they also submitted a request for Watson's arrest to German authorities.