Militant environmentalists said they had pelted stink bombs at a Japanese whaling ship in Australian waters in their latest bid to disrupt hunting of the protected creatures.

The Sea Shepherd Conservation Society said it "pursued and delivered 10 bottles of rotten butter and 15 bottles of a methyl cellulose and indelible dye mixture" to the Kaiko Maru vessel Friday evening.

A Japanese government-backed whaling body claimed that the activists' ship rammed into the left side of the Japanese vessel, damaging a bulwark.

"We cannot tolerate disruptive activities that threaten the safety of the crew members," Minoru Morimoto, head of the Institute of Cetacean Research, which carries out Japan's whale hunting operations, said in a statement.

Sea Sepherd said in an online statement however it was the Japanese ship that "steered hard" and struck the group's ship "Steve Irwin", although neither vessel suffered serious damage.

Paul Watson, the captain of the activists' ship, said in the statement that his crew was trying to push the Japanese whalers out of Australian waters. Sea Shepherd is an international group with headquarters in the United States and Australia.

Japan kills hundreds of whales a year in the name of research despite an international moratorium on commercial whaling.

Tokyo makes no secret of the fact that the meat ends up on dinner tables and accuses Westerners of insensitivity to its whaling culture.

For the past four years Watson has led a Sea Shepherd vessel trying to impede the whaling ships during their hunting season.

Watson claimed earlier this year that his ship's hounding of the Japanese whalers last season had saved the lives of 500 of the giant mammals.

But the activists' repeated attacks have led Japan to label them as "terrorists."

After an earlier attempt to pelt a Japanese harpoon boat with stink bombs, Watson told AFP on Monday that the activists would continue trying to hamper the whalers.

"We will just harass them, blockade them, do everything to prevent them from resuming whaling," he said at the time.

"Most likely they will run and we will chase and they'll run and we'll chase and that's fine. As long as they are running they are not killing whales."