Japanese whalers say Sea Shepherd crews sabotaged a refuelling process in the Southern Ocean, causing several collisions.
The Institute of Cetacean Research (ICR) has responded to claims by the anti-whaling group that a Japanese whaling ship collided with two of their protest vessels.
ICR says two Sea Shepherd ships made "foolhardy obstruction attempts", repeatedly coming within close quarters of the Nisshin Maru and its supply tanker.
It says the Steve Irwin, Bob Barker and Sam Simon vessels "provoked several collisions" and the Nisshin Maru sustained minor damage.
The Japanese vessel "used its water pump as a preventive measure", the ICR said.
It said the Nisshin Maru decided to interrupt the refuelling operation due to the "extremely dangerous behaviour" of the Sea Shepherd vessels.
And the ICR denies allegations there was oil spillage during the refuelling process.
Earlier the anti-whaling activists called for Australia to send a naval vessel to the Southern Ocean after the confrontation led to their flagship vessel being damaged.
"The Nisshin Maru has rammed the Steve Irwin and the Bob Barker, but both vessels continue to hold their positions," Paul Watson, the founder of the Sea Shepherd Conservation Society which runs the protest boats, said.
Watson also accused Japanese coastguard personnel of throwing concussion grenades at their protest ships during a confrontation in the frigid waters near Antarctica and said the Bob Barker was taking on water in its engine room at one stage.
Sea Shepherd director Bob Brown said the two Sea Shepherd ships had been repeatedly rammed as activists were attempting to prevent the 8,000-tonne Japanese factory ship Nisshin Maru refuelling from a tanker, Sun Laurel.
Japan introduced scientific whaling to skirt a commercial whaling ban under a 1986 moratorium. It argues it has a right to monitor the whales' impact on its fishing industry.