The organisation in charge of Japan's scientific whaling program has accused the Sea Shepherd conservation group of endangering its crews in the Southern Ocean.

The two sides have clashed for the first time during this season's Antarctic hunt.

Militant anti-whaling activists from the Sea Shepherd group say they have begun pursuing the Japanese whaling fleet through the icy waters of the Antarctic.

They say the whaling ships used water cannons on their inflatable boats during high-speed chases.

But the Institute of Cetacean Research, which runs Japan's scientific whaling program, accused the Sea Shepherd activists of throwing glass bottle projectiles and deploying ropes to try and foul the propeller and rudder of one of its ships.

It has accused the group of dangerous and violent tactics, calling on Australia and the Netherlands to take criminal action against the activists.

At least two ships in the Sea Shepard fleet are registered in the Netherlands.

But Sea Shepherd Society's president Paul Watson is undeterred.

"We'll stay on them for two and a half months - if we chase them every day then they're not going to kill any whales," he said.