The Sea Shepherd said the bow was sheared off the Ady Gil
Anti-whaling activists have accused a Japanese vessel of ramming their high-tech speed boat during a confrontation in the Southern Ocean.
Video of the incident appeared to show the Japanese ship severely damaging the Ady Gil, but all six crew were rescued.
Earlier the campaigners - who are trying to stop Japan's whaling fleet - said they threw chemicals onto the whaling boat to prevent it being used.
The whalers said the activists tried to tangle their propeller with a rope.
In recent years the two sides have regularly confronted each other in the waters around the Antarctic.
Sea Shepherd spokesman Paul Watson said the incident had turned the confrontations between the whalers and the activists into a "real whale war".
A statement on the Sea Shepherd website said a Japanese vessel that was accompanying the Nisshin Maru whaler "deliberately rammed" the Ady Gil, a high-tech speed boat that resembles a stealth bomber, shearing off its bow.
The crew of the Ady Gil, five from New Zealander and one from the Netherlands, were picked up unharmed by nearby Sea Shepherd vessel Bob Barker near Commonwealth Bay.
"The Ady Gil is believed to be sinking and chances of salvage are very grim," the Sea Shepherd statement said.
A video apparently shot from on board the Japanese vessel showed the two ships smashing into each other at speed.
The Ady Gil was swamped by waves, its nose was torn off and damage could be seen to its side.
Japan's Institute of Cetacean Research (ICR), which conducts the country's whale hunt, accused Sea Shepherd of using the Ady Gil to attack its vessels.
Confrontations between whalers and activists have heated up over recent years
They alleged the trimaran speedboat came dangerously close to the Nisshin Maru, trying to entangle its rudder and propeller with a rope and launching stink bombs at the vessel.
"The Sea Shepherd extremism is becoming more violent... Their actions are nothing but felonious behaviour," the (ICR) said in a statement.
Japan's fisheries agency said it was the fourth time this season that the anti-whaling activists had interfered with the whaling fleet's operations, Kyodo news agency reported.
The Sea Shepherd group sends boats to Antarctic waters each year to try to stop the Japanese whaling fleet hunting whales.
Japan abandoned commercial whaling in 1986 after agreeing to a global moratorium but international rules allow it to annually kill hundreds of whales under the auspices of a research programme.
Conservationists say the whaling is a cover for the sale and consumption of whale meat.