Sea Shepherd have claimed they were ambushed under the cover of darkness Sunday by a Japanese whaling fleet in a "ruthless assault" to disable their ship.
Whalers trailing steel cables are said to have launched another attack on a Sea Shepherd vessel, forcing it away from a Japanese factory ship in the Antarctic.
The conservationists said their ship, Bob Barker, was subjected to the night-time attack, after it had managed to steam within six nautical miles of the Nisshin Maru.
In the confrontation off Cape Adare in the Ross Sea, two harpoon ships crossed the bow of the Bob Barker a total of 33 times at close range trailing the cables in what Captain Peter Hammarstedt said was an attempt to disable the ship's propellor and rudder.
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"I radioed the harpoon ships to let them know that our operations are completely lawful and that any aggressive action on their part would be reported to the Australian government and New Zealand Search and Rescue," Mr Hammarstedt said.
The whalers also blinded the Bob Barker's bridge with powerful searchlights, impairing vision and endangering navigation, Sea Shepherd Australia said in a statement.
Mr Hammarstedt said federal Environment Minister Greg Hunt had been contacted about the attack.
"I have nine Australians and one New Zealander on board as part of my brave crew who have endured this ruthless assault," he said.
"My message is very clear to all parties - all sides must absolutely abide by international maritime law," he said.
It was the second time in three weeks that the Bob Barker has undergone such a confrontation.
After the last engagement, the Fisheries Agency of Japan said: "The sabotage activities of the Sea Shepherd are acts of extreme danger which threaten the safety of Japanese research vessels and lives of their crew."
Managing Director of Sea Shepherd Australia, Jeff Hansen, said, “The Bob Barker is in the Southern Ocean to defend the Southern Ocean Whale Sanctuary from the illegal Japanese whalers.
"Both Australia and New Zealand are parties to the Sanctuary. Both the Australian and New Zealand governments have legally challenged the Japanese whaling operations at the International Court of Justice.
"So where are these governments now, when their citizens and the Sanctuary are under attack from these poachers?”