Tokyo will seek Interpol's help to arrest Canadian Paul Watson for ordering his crew to harass whaling ships in clashes in which Japanese crew were allegedly injured by rancid butter projectiles, broadcaster NHK reported.
Watson, speaking in New York, said "the arrest warrant is just totally political, it's nothing. I'm not concerned, and Interpol is not going to extradite me on a politically motivated charge."
"We save whales, and we are going to continue to go down to the southern ocean," the 59-year-old environmental campaigner and captain of the group's Steve Irwin vessel told reporters in comments broadcast in Japan.
The reported arrest warrant and Interpol request, which the Japan Coast Guard declined to confirm, are the latest act in a long-running battle between Japan and the US-based Sea Shepherd Conservation Society.
Japan hunts whales under a loophole to an international moratorium that allows the killing of the sea mammals for scientific research and does not hide the fact that the meat is later sold in shops and restaurants.
Sea Shepherd has sought to obstruct Japan's whalers for years and this year said they had their most successful season yet by preventing the harpoon ships from killing hundreds of the ocean giants.
Japanese authorities say the activists injured Japanese crew with chemical burns by throwing bottles of butyric acid, which the Sea Shepherd group describes as rancid butter stink bombs.
Japan's Fisheries Minister Hirotaka Akamatsu said "Japan should take decisive action. We should not leave such cases hanging in the air. Regardless of whether they are pro- or anti-whaling, what they did was a crime."
In one of the clashes, the Sea Shepherd's futuristic powerboat the Ady Gil, carrying six crew, was sliced in two in a collision with the whaling fleet's security ship the Shonan Maru II in January. It later sank.
The Ady Gil's captain Peter Bethune, 45, subsequently boarded the Shonan Maru II from a jet ski with the stated intent of making a citizen's arrest of its captain for attempted murder and to present him with a bill for the boat.
Bethune, a New Zealander, was detained and is now under arrest awaiting trial for trespass, causing injury, vandalism, carrying a knife and obstructing commercial activities. If convicted who could face up to 15 years jail.