The Japanese government and conservation group Sea Shepherd have each blamed the other for a collision in the Southern Ocean.

Sea Shepherd Australia says the Japanese ship Yushin Maru deliberately crashed into its Bob Barker vessel, damaging the bow and anchor.

The Japanese government says a collision happened after Sea Shepherd vessels deliberately tried to sabotage their whale research fleet.

The incident comes eight days after the Sea Shepherd fleet blocked the slipway of Japanese factory vessel Nisshin Maru, suspending whaling activity.

Captain Peter Hammarstedt of the Bob Barker says the ship received some damage when the Yushin Maru crossed its bow just before 7:00am (AEDT) today.

Captain Hammarstedt says the Steve Irwin vessel was also "attacked".

"The Sea Shepherd ships Steve Irwin and Bob Barker were both unprovokedly attacked by three harpoon ships belonging to the Japanese whale poaching fleet," he told the ABC.

"These harpoon ships came in heavy and hard. They hit my bow with about 300 metres of steel cable with the express intent of causing damage to my rudder and propellers.

"Thankfully because of a lot of evasive manoeuvring I was able to avoid being entangled, but on one occasion one of the harpoon ships came so close that they ended up colliding with my vessel."

Sorry, this video has expired Japanese whaling fleet's claim 'an absolute lie': Sea Shepherd ( Interview by Virginia Trioli )

Captain Hammarstedt says the collision caused significant damage to plating and framework that will have to be repaired once the Bob Barker returns to port.

However, in a statement issued through the Japanese embassy in Canberra, the country's Institute of Cetacean Research says activists dragged ropes in front of the Japanese fleet, and the Bob Barker rammed into one of the Japanese ships.

This morning, Sea Shepherd spokesman Sid Chakravarthi has hit back, saying: "It's an absolute lie."

Mr Chakravarthi admits Sea Shepherd did use steel ropes to try to stop the whaling ship, but says it was in self-defence.

The Federal Government says it is seeking more details about the reported collision.

Environment Minister Greg Hunt says Japanese whaling ships and anti-whaling protestors must both abide by international law.

"These are dangerous waters nobody can play any games with safety," he said.

"Nobody can play any games with international maritime law everyone must abide by the law and of course if there is evidence that either party has breached international maritime law we will raise it."