Sunday night's confrontation between Japanese whalers and Sea Shepherd activists.

A confrontation between Japanese whalers and Sea Shepherd activists. Photo: Simon Ager/Sea Shepherd Australia

Japan's whalers expect to return to the Antarctic, despite losing an International Court of Justice case brought against them by Australia banning their current hunt.

Tokyo's Institute of Cetacean Research wants to go back to the Southern Ocean for a continuing "research program" after missing next summer, a court document filed in the United States says.

The new program would comply with the ICJ decision, according to a filing made for the institute to a United States District Court in a case against the Sea Shepherd Conservation Society.

Sea Shepherd founder, Paul Watson, said: "They're going to do lethal whaling. They need the meat to send back to pay for it."

The ICJ found that Japan's Antarctic whaling program, called JARPA II, was not scientific research as permitted under International Whaling Commission rules.

Instead the ICJ meeting in The Hague concluded on 31 March that JARPA II violated the IWC's global moratorium on commercial whaling.

"It is to be expected that Japan will take account of the reasoning and conclusions contained in this judgement as it evaluates the possibility of granting any future permits," the ICJ said.

Prime Minister Tony Abbott said after the decision he "absolutely appreciated" Australians' desire to see an end to Southern Ocean whaling.

"It's now up to Japan to appropriately reflect on the judgment and I'm sure that's exactly what will happen," Mr Abbott said.

Japanese Prime Minister Shinzo Abe said he was deeply disappointed with the ruling, but would abide it, according to the country's chief ICJ negotiator, Koji Tsuruoka.

Shortly afterwards the Fisheries Agency of Japan said it would cancel planned "research whaling" next Antarctic summer because of the ICJ ruling.

This meant that for the first time in more than a century, the Antarctic would have a summer free of any whaling.

The Institute of Cetacean Research disclosed plans to go south again in a pleading filed with the U.S. court in Seattle on Saturday, Australian time, in a case against Sea Shepherd's harassment of the whaling fleet.

"The Government of Japan recently announced the JARPA II special permits would not be issued for Plaintiffs to conduct research in the Southern Ocean during the 2014-15 season," said the filing by John Neupert, counsel for the plaintiff ICR.

"For the information of the Court and parties, Plaintiffs expect that they will be conducting a Southern Ocean research program for subsequent seasons that would be in accord with the ICJ decision," Mr Neupert said.

Senior Australian scientist Tony Press, who observed the ICJ case, said its judgement focussed on what constituted a proportionate hunt under IWC rules.

The judgement made a series of points about the size of the take, about lethal versus non-lethal research, and about the length of the program, said Dr Press, director of the Antarctic Climate and Ecosystems Co-operative Research Centre.

"The ramifications are that Japan, or anybody else who wants to go...lethal scientific whaling, had better go and have a very good look at the judgement," Dr Press told a University of Tasmania forum.

The whaling fleet returned to Japan last week having killed 251 minkes, a fraction of its 935 minke target, under pressure from activists in a campaign managed by Sea Shepherd Australia.

ANU Professor of International Law Don Rothwell said the ICR's move was significant as the first affirmative statement from Japan that it intended to continue with some kind of scientific program.

But he cautioned that it needed to be read in the light of the institute's US legal action, which might go against the ICR if there were no further whaling plans.  

"This keeps their options open before that US court," Professor Rothwell said.