Greenpeace task force leader Shane Rattenbury said his ship, the Arctic Sunrise, was carrying 25 people when it was rammed by the Nisshin Maru, a factory ship belonging to a Japanese whaling fleet in what he called a "deliberate action."
Greenpeace said the whaling ship was watching over activists onboard inflatable rafts as they graffitied the words "whale meat from sanctuary" on the side of a nearby Japanese supply vessel, shortly before the collision occurred.
Greenpeace supplied photos of its damaged ship, but the cause of the destruction couldn't be independently verified. The Japanese Embassy was not immediately available for comment Sunday.
The Arctic Sunrise has been harrasing the Japan's whaling fleet in Antarctic waters for almost two weeks, hampering their hunt for 850 minke whales and 10 fin whales as part of Japan's scientific research program.
The research whaling is permitted under the rules of the International Whaling Commission, but Australia and other anti-whaling countries say it is really commercial whaling in disguise.
Environmental groups have been repeatedly denied permission by a federal court to sue a Japanese whaling company for allegedly killing minke whales in Antarctic waters, which the Australian government has unilateraley declared a whale sanctuary.
The courts have ruled that Australia cannot legally stop a whaling company hunting in international waters, because Japan doesn't recognize Australia's jurisdiction over international waters.
The Sea Shepherd Conservation Society has threatened it will purposely damage Japanese ships in their effors to prevent whaling.
"We anticipate that we may sustain some damage but our objective is to shut down their illegal activities and we will risk losing the ship if need be to further that objective," he wrote.
"The crew are ready and eager to engage the Japanese whalers," he added.