A hi-tech anti-whaling speedboat resembling a stealth bomber had its bow sheared off and was taking on water today after it collided with a Japanese whaling ship in Antarctica.

The six crew members of the Sea Shepherd Conservation Society speedboat were safely rescued.

The clash was apparently the most serious in the past several years, during which the marine conservation group has sent vessels into far southern waters to try to harass the Japanese fleet into ceasing its annual whale cull.

The society said its boat the Ady Gil was hit by the Japanese ship the Shonan Maru near Commonwealth Bay and had its bow sheared off.

"The condition of the Ady Gil now is that it is inoperable and the crew of the Ady Gil has been transferred to our other vessel, the Bob Barker," Locky Maclean, the first mate of the society's lead ship told Australian Broadcasting Corpation radio.

The Ady Gil's captain had stayed on board to try to save equipment "before it floods too severely," he said.

Clashes using hand-thrown stink bombs, ropes meant to tangle propellers and high-tech sound equipment have been common in recent years, as have collisions between ships.

Japan's fisheries agency, which has no direct involvement in whaling but oversees Japanese fishing operations, said it was still checking details about the clash.

"We have confirmed that there was a collision, but we have no other details. We have not heard that any boats have sunk. We are now trying to confirm details of why the collision occurred," said a fisheries agency spokesman, Toshinori Uoya.

He said there were no injuries on the Japanese vessel, but said he was not sure about the Ady Gil crew members.

Sea Shepherd sends boats to Antarctic waters each southern summer to try to stop the Japanese fleet killing whales under what the fleet calls a scientific whaling programme. Conservationists and many countries say the programme is a front for commercial whaling.

Earlier today, the Institute of Cetacean Research (ICR), the non-profit organisation that conducts the hunt, said that one of the ships in the whaling fleet was attacked by the Ady Gil, but it did not mention a collision.

It said the Ady Gil arrived on the scene at about 6pm GMT yesterday and that its crew threw ropes at the whaling lead ship, the Nisshin Maru. It said another Sea Shepherd vessel, the Bob Barker, had already arrived in nearby waters.

The Ady Gil came "within collision distance" of the Nisshin Maru's bow and repeatedly dangled a rope in the water in an attempt to entangle the ship's rudder and propeller, and lobbed small projectiles designed to release a foul smell, said the ICR. The whalers responded by firing high-powered hoses to keep the Sea Shepherd vessels away.

"The obstructionist activities of the Sea Shepherd threaten the lives and property of those involved in our research, are very dangerous and cannot be forgiven," the ICR statement said.

Each side routinely alleges the other engages in dangerous activity. Australia and New Zealand – which have Antarctica territories – have urged both sides to show restraint, warning that they are far from rescue if anything goes wrong.

Japan's whaling fleet left in November for its annual hunt in the Antarctic waters. Uoya said that for security reasons, details of the fleet's composition, the number of whales it hoped to take and the number of crew members was not being released.