Paul Watson, who was on the group's main vessel, the Steve Irwin, about 500 miles away, said the confrontation took place in Australian waters, The Times of London reported. He said the six men in the crew of the Ady Gil were rescued.
"This seriously escalates the whole situation," Watson said.
The Ady Gil is a lightweight 79-foot trimaran built at a cost of $1.5 million to harass Japanese ships. The Institute of Cetacean Research, the Japanese agency responsible for that nation's whaling science, reported on its Web site the Ady Gil had been firing projectiles at a Japanese vessel and trying to entangle its propellers, Watson said.
The Shonan Maru, a ship providing security for the fleet, allegedly rammed the Ady Gil.
Australian Environment Minister Peter Garrett recently said he had warned both anti-whaling protesters and the Japanese of the risk of nautical confrontations, especially in the icy waters near Antarctica.