Mr Watson said the arrest warrant was politically motivated
The Japanese coastguard has obtained an arrest warrant for Canadian environmental activist Paul Watson for disrupting whale hunts, reports say.
Mr Watson's Sea Shepherd Conservation Society shadowed the annual Japanese whaling fleet through the Antarctic.
He advocates direct action and has faced charges in Canada and Norway.
Japan hunts hundreds of whales each year for what it calls research, but environmentalists say the real purpose is to sell whale meat.
Sea Shepherd's campaign saw its vessels manoeuvring close to Japan's whaling ships during their annual hunt in the Southern Ocean.
In January, one of its boats was destroyed in a crash with a Japanese harpoon vessel. Sea Shepherd says the incident has not been properly investigated.
The Japan Coast Guard obtained an arrest warrant in Tokyo against Mr Watson for allegedly instructing members of his group to obstruct Japan's whaling mission and causing injury to Japanese crew, Japanese media reported.
National broadcaster NHK also reported that Japan would seek the 59-year old Canadian's arrest through the International Criminal Police Organisation (Interpol).
The Japanese Coast Guard declined to confirm the reports.
Confrontations between Japanese whaling ships and the activists during the recent whaling season near the Antarctic has already led to the arrest of a New Zealand anti-whaling activist who boarded a Japanese harpoon ship.
Pete Bethune, also of the Sea Shepherd Conservation Society, boarded the Shonan Maru 2 in February, and tried to make a citizen's arrest of its captain.
If found guilty of five offences, including trespass and causing injury, Mr Bethune could face up to 15 years in prison.
Mr Bethune had been in command of Sea Shepherd's hi-tech speedboat, the Ady Gil, when it was destroyed in a collision with the Shonan Maru 2 in January. All six crew members escaped unharmed.
The crew of the Shonan Maru said the activists had tried to tangle a rope in their propeller and had thrown butyric acid at the ship, giving a "chemical burn" to one sailor.
But Sea Shepherd has denied any of its activists caused injury and said the substance thrown was harmless, if unpleasant, rancid butter.
Mr Watson accused Australia, New Zealand and Japan of failing to investigate the collision or question the captain of the Shonan Maru.
In a statement on the Sea Shepherd website, he questioned why the arrest warrant had been issued now when the group had been "obstructing whaling operations since December 2005".
He said there was "no doubt that the motives of the Japanese Coast Guard and the Japanese government are political".
"The Japanese government is desperate to stop the Sea Shepherd ships from returning to the Southern Ocean Whale Sanctuary for the 2010 and 2011 season," he said.
Japan abandoned commercial whaling in 1986 after agreeing to a global moratorium - but international rules allow it to continue hunting under the auspices of a research programme.