The Japanese embassy in Berlin said in a statement sent to news agency AFP that it had given the German foreign ministry documents on July 19 "with which the Japanese coast guard requested the detention of Paul Watson with the aim of extraditing him to Japan."
In a complex legal odyssey spanning the globe, Costa Rica filed its own extradition request against Watson on charges stemming from a high-seas confrontation between a Sea Shepherd ship and a Costa Rican vessel over alleged illegal shark finning in 2002.
Watson, a Canadian national, was accused of "putting a ship's crew in danger." But he could face more serious charges in Japan as Sea Shepherd has long been known for aggressive attacks on Japanese whalers.
The 61-year-old was arrested at Frankfurt airport in May and detained for a week before being released on bail after paying €250,000 ($306,500) and being ordered to appear before police twice a day.
However this week, a Frankfurt court reported that Watson had skipped bail on July 22 and quoted his lawyer as saying he had left Germany for "for an unspecified destination." It then reissued an arrest warrant for him.
Sea Shepherd suggested on Thursday that Watson had fled Germany because he feared Japan would seek his extradition if he were sent to Costa Rica. The group said it had no idea of his whereabouts.
The Japanese embassy insisted in its statement Friday that it had nothing to do with Costa Rica's legal proceedings against Watson.
"The extradition request from Costa Rica is a matter that only concerns Germany and Costa Rica," it said. "Japan is unable to comment."
Watson, who was tweeting as recently as Tuesday but made no mention of where he was or what he planned to do, has previously suggested that Japan might be "putting pressure" on Germany to carry out the extradition order.
Sea Shepherd is best known for its annual pursuit of the Japanese whaling fleet in Antarctica, using increasingly militant methods to halt the hunt, including the boarding of vessels.
This year, after setting off from Australia, the group hurled stink bombs at the boats on the high seas and used ropes to try to tangle their propellers in a series of exchanges which saw the whalers retaliate with water cannon.
The whaling fleet killed less than a third of the animals it planned to because of the sabotage attempts.