The captain of the Sea Shepherd Conservation Society ship, Paul Watson holds a bullet and a bent badge, from aboard the anti-whaling vessel. -- PHOTO: AP

The captain of the Sea Shepherd Conservation Society ship, Paul Watson, said he was shot in his bullet-proof vest, although Australian Foreign Minister Stephen Smith said Japanese officials insisted only warning devices were fired.

'What hit me was a bullet, it wasn't a flash grenade. We pulled it out of the vest,' Mr Watson told ABC radio.

He said the crew of the Sea Shepherd's ship Steve Irwin was throwing stink bombs at the whaling ship Nisshin Maru when coast guards posted on the Japanese vessel responded with flash grenades.

He said he felt a thud during the confrontation and later found a bullet lodged in his kevlar vest, which he said hit with enough force to bend a badge he was wearing under the protective device and bruise his chest.

'If I wasn't wearing the vest, it would have been pretty serious,' he said.

Mr Watson did not detail the injuries of the crew member he said was hurt by a flash grenade.

Mr Smith said Japan initially advised Australian officials that shots had been fired but later clarified details of the incident.

'Japanese officials have now advised the Australian embassy in Tokyo that during the incident in the Southern Ocean this afternoon, three warning balls - also known as flashbangs - had been fired,' Mr Smith said in a statement.

'Japanese officials have advised that these devices are designed to make a loud noise but not to injure, and that no gunshots had been fired.'

The latest clash comes after Sea Shepherd activists on Monday hurled stink bombs onto the Japanese whaling ship, slightly injuring three crew and coast guard members on board, according to Japan.

The Sea Shepherd said it threw rotten butter. Japanese officials described the substance as butyric acid, which is stinging to the eyes.

In January, a pair of Sea Shepherd protesters were held for two days after boarding a Japanese whaler before being handed over to an Australian customs vessel, then returning to the Steve Irwin.

Japan kills up to 1,000 whales a year using a loophole in a 1986 global moratorium on whaling that allows 'lethal research' on the giant mammals.

Australia has led international diplomatic efforts to end the cull but Smith said he condemned actions by crew members of any vessel that could cause injury.

'The Australian government once again calls on all parties in the Southern Ocean - including all protest and whaling vessels, and their respective crews - to exercise restraint,' he said.

'The Australian government strongly discourages activity which could be illegal, or unsafe activity which could lead to injury or loss of life at sea.'

Mr Watson said the latest confrontation would not stop Sea Shepherd's efforts to disrupt the whaling season, which still has about two weeks to run.

'It won't deter us from trying to stop their illegal activities, no,' he said.

'We'll take more precautions but we'll certainly not stop pursuing them.' -- AFP