Anti-whaling activists claim two of their vessels have been "rammed" by a Japanese boat in the Southern Ocean.

The Sea Shepherd group alleges the Japanese factory boat Nisshin Maru deliberately collided with their ships, the Steve Irwin and the Bob Barker.

They also claim Japanese coast guards are throwing "concussion grenades" towards the fleet.

"The Nisshin Maru has rammed the Steve Irwin and the Bob Barker but both vessels continue to hold their positions," Sea Shepherd Captain Paul Watson said in a statement on Facebook.

"The Bob Barker is taking on water in their engine room."

The Japanese Institute of Cetacean Research has been contacted for comment.

More to follow.