No one was injured, though both ships received minor damage in Sunday's collision – the latest drama in an annual battle between the conservationists and the whalers.
Sea Shepherd, which each year tries to harass the whaling fleet into ending its hunt, said they were the victims of a lengthy attack by the whalers.
The protest group said the whaling vessels spent hours repeatedly dragging steel cables across the bows of the Sea Shepherd's ships in a bid to damage the rudders and propellers.
Japan's Yushin Maru No. 3 then struck Sea Shepherd's Bob Barker when it crossed too closely in front of the protest ship, damaging its bow and anchor, said Peter Hammarstedt, captain of the Bob Barker.
"It was an unprovoked attack and they did so ruthlessly," Hammarstedt told The Associated Press by satellite phone from the Bob Barker, named after the famous "The Price is Right" game show host who donated millions of dollars to the group.
Japan, meanwhile, says Sea Shepherd is to blame. The Tokyo-based Institute of Cetacean Research, which sponsors the annual whale hunt, said in a statement that protesters on board two inflatable boats from the Bob Barker dropped ropes in front of the bow of the Yushin Maru, which became entangled in the ship's propeller.
The Bob Barker then drew too close to the Yushin Maru No. 3, colliding with its stern and damaging the whaling ship's hull and railing, the institute said.
"Our research whaling is a legitimate activity allowed under the international treaty. Sea Shepherd's violent sabotage against it, which is threatening the lives of the Japanese crew-members and causing damage to our ships and equipment, cannot be tolerated," Japan's Fisheries Agency said in a statement.
Australia's Federal Environment Minister Greg Hunt on Monday ordered an investigation into the collision.
Japan, which plans to kill about 1000 whales this year, is allowed to hunt the animals for scientific purposes under an exception to a 1986 ban on whaling.
Critics say the programme is a cover for commercial whaling, because whale meat not used for study is sold as food.
Last year, Australia went to the United Nations' highest court in a bid to outlaw Japan's annual whale hunt. Japan says the hunt is legal and produces valuable scientific data. The International Court of Justice is expected to issue its decision later this year.