Whale conservation group Sea Shepherd has rejected claims it threw illegal stun grenades onboard a Japanese whaling ship in the Southern Ocean earlier this month.

The Japanese Institute of Cetacean Research, which organises Japan's so-called scientific whaling program, has released footage showing activists onboard boats belonging to the Sea Shepherd Conservation Society throwing objects onto the Yushin Maru 2.

The two sides have already clashed twice this year during the annual Antarctic hunt, and the Japanese institute says at least two stun grenades and one smoke bomb were thrown in the most recent incident, with one of the grenades landing on protective nets on its harpoon ship.

But Sea Shepherd captain Paul Watson says the anti-whaling activists use only smoke and stink bombs in their mission to prevent the killing of whales.

"We couldn't have thrown flash bangs [grenades] on the ship, we don't have them, it's prohibited," he said.

"We couldn't even bring them into Australia if we wanted to, so they certainly don't have any evidence of us doing that because we simply didn't do it.

"They throw concussion grenades at us, they shoot at us, they destroy our ships, they throw long-range acoustical weapons at us.

"When we throw a stink bomb back at them they act all confused and upset and shocked, I mean it's amazing."

The Japanese fleet is in Antarctic waters harpooning whales for what it says is scientific research, but opponents of the hunt say it is a cover for commercial harvesting.

The most recent clash follows an earlier attack by the Sea Shepherd's other ships Steve Irwin and Bob Barker against the Japanese whaling ship Yushin Maru 3 in Antarctic waters on New Year's Day.

Prime Minister Julia Gillard has called for calm in the wake of the recent skirmishes, saying all ships need to act responsibly in the dangerous waters.

"This is a remote, inhospitable, dangerous place [and] everybody has to act responsibly," she said.

"Any sense that somehow you can act irresponsibly and somehow someone miraculously turns up to save you - that is not the way the world works.

"These are dangerous waters and people need to conduct themselves responsibly in any protest activity and all vessels need to conduct themselves responsibly."

But Mr Watson says the use of smoke and stink bombs is not a dangerous tactic.

"We've never injured anybody, we don't intend to injure anybody," he said.

"We've been doing the same thing for five to six years, the Japanese whalers respond every time. It's the first time we've done it to them, I think they're being a little overly dramatic."

Mr Watson says his group's pursuit of the Japanese fleet has resulted in few, if any, whales being killed so far.