Protesters from the Sea Shepherd Conservation Society have backed away from their intense clash with whaling vessels in the Southern Ocean, but say they'll return next year with a longer range ship.

Steve Irwin captain Paul Watson said after deciding to return to Australian shores yesterday, ''We need to block those deadly harpoons and we need to outrun these hunter killer ships and to do that I need a ship that is as fast as they are and I intend to get one and I intend to return next year.''

The decision ends a season of extreme clashes between whalers and protesters, with some saying confrontations were the most intense seen in the past five years.

In the most recent incident last Friday, the Steve Irwin rammed the Yushin Maru 2 as it was hauling on board a minke whale, and the Yushin Maru 3 as it tried to transfer its catch to the mother ship.

The Japanese said the protesters had deliberately masterminded the collisions, but Mr Watson said the manoeuvring of the whalers had made it impossible to avoid the crashes.

He said the Japanese used water cannon and a noise weapon against protesters in the skirmish, leaving three protesters with minor injuries.

Mr Watson declared the season a success, saying the society's interference had cost the whalers money, hampered their operations and saved the lives of a good many whales.

But Glenn Inwood from Japan's Institute of Cetacean Research said the Dutch-registered protest ship had engaged in serious acts of violence that put lives at risk.

''The Netherlands and Australia need to examine closely their roles in allowing Watson to commit these maritime crimes,'' he said.

''If he returns next year, its quite possible someone will be killed.''

The Steve Irwin is expected to arrive back in Australia in the the next two weeks, before it can be intercepted by a Japanese security vessel, the Taiyo Maru No 38, which Mr Watson says is en route to intercept the protest ship and seize its video footage of whale kills. AAP