Stink bombs, paint and tear gas were fired from ship to ship in the latest violent clash between whalers and activists in the Southern Ocean.

The Japanese Fisheries Agency said the whaling boat Yushin Maru 2 was confronted during its annual hunt by the Sea Shepherd vessel Steve Irwin yesterday.

It claimed the anti-whaling protesters used a high-powered launcher to fire 20 glass bottles containing paint and butyric acid.

Butyric acid, which is found in parmesan cheese and vomit, has a foul smell and is commonly used in stink bombs.

"YS2 gave warnings, by voice and water cannon, to the obstructive activities," the agency said.

It called Sea Shepherd's actions "extremely dangerous acts which threaten the safety of our country's vessels and the life of its crew".

The captain of the Steve Irwin, Paul Watson, told ABC radio the whalers responded by throwing sticks and tear gas.

"They have been using concussion grenades on us," he said.

"Today they used, also for the first time, tear gas, which they have in these large canisters on backpacks."

No one was injured in the latest clash, which comes only a week after a similar attack by the Sea Shepherd.

In that incident, the activists said three of their members were injured when Japanese crewmen used grappling hooks and bamboo poles against them.

The annual clash of words and weapons began on December 6, when the Japanese whaling fleet left the port of Shimonoseki with beefed up security in response to last year's drama.

The whalers aim to catch around 900 minke and fin whales for what Japan says is scientific research".