Paul Watson, who holds dual Canadian and U.S. citizenship, issued a statement saying he was stepping down from the Sea Shepherd Conservation Society in order to comply with an injunction handed down by a Seattle court last month.
The 9th U.S. Circuit Court of Appeals ordered the organization to stay at least 457 metres away from Japanese whaling vessels off Antarctica.
Watson's statement of resignation said he was personally named in the injunction, which was meant to prevent the vocal activists from carrying on with their annual efforts to stall the whale hunting season.
His decision to step down, he said, came from a desire to maintain a clean record.
"I myself have never been convicted of a felony crime," Watson said in the statement. "And for this reason, the Sea Shepherd Conservation Society in the United States and myself as a U.S. citizen must comply with the order by the 9th Circuit court of the United States."
Watson said he was resigning from all positions he held with Sea Shepherd's U.S. and Australian chapters and as captain of one of the group's vessels.
Watson said the anti-whaling campaign will continue under the leadership of former Australian senator Bob Brown, adding he himself will participate only as an observer under the terms of the injunction.
Whalers with Japan's Institute of Cetacean Research sued Sea Shepherd last year to prevent the protesters from interfering with their annual hunt, but the judge refused to grant the request. The whalers appealed, and a three-judge panel of the 9th Circuit late Monday ordered Sea Shepherd not to attack or approach any of the Japanese vessels until it can rule.
Japan's whaling fleet kills up to 1,000 whales a year, as allowed by the International Whaling Commission. Japan is permitted to hunt the animals as long as they are killed for research and not commercial purposes.
But whale meat not used for study is sold as food in Japan, and critics say that's the real reason for the hunts.
Sea Shepherd activists use stink bombs, lasers and other non-lethal means to interfere with the whalers. The group argues that its activities are supported by international law and that U.S. courts don't have jurisdiction in the waters off Antarctica where the hunt occurs.
It's not the first time Watson runs into trouble with the law.
In July, the 62-year-old fled from Germany after being arrested at the behest of the Costa Rican government, which is pursuing him on a warrant that claims he endangered a fishing vessel crew in Guatemalan waters in 2002.
Watson contends the Costa Rican charges were filed because of pressure from the Japanese government and that he eventually would have been extradited to Japan if he had remained in custody.
Watson, who was born in Toronto, left Greenpeace in 1977 to set up the more action-oriented Sea Shepherd. The group has waged aggressive campaigns to protect whales, dolphins and other marine animals, prompting Japanese officials to label its members terrorists and seek Watson's arrest.