The International Court of Justice has upheld Australia's bid to ban Japan's Antarctic whaling program.

ICJ president Peter Tomka said the court concluded the scientific permits granted by Japan for its whaling program were not scientific research as defined under International Whaling Commission rules.

Mr Tomka said in The Hague that the court was persuaded that Japan had conducted a program for logistical and political considerations, rather than scientific research.

The court unanimously found it had jurisdiction to hear the case, and by 12 votes to four found that special permits granted by Japan in connection with the program, JARPA II, did not fall within the IWC convention.

It therefore ordered that Japan revoke any scientific permit under JARPA II and refrain from granting any further permits.

On Monday Japan said it would respect the ruling despite "deep disappointment" with the landmark decision.

"As a state that respects the rule of law ... and as a responsible member of the global community, Japan will abide by the decision of the court," Japan's chief negotiator Koji Tsuruoka said outside the United Nations' top court in The Hague.

With Prime Minister Tony Abbott due to visit Japan next week, Attorney-General George Brandis was quick to calm any threat of a diplomatic storm that might hurt Australia and Japan's relationship following the court's decision.

Senator Brandis stressed that the two nations had been in dispute on just the single issue of whaling.

Former Labor environment minister Peter Garrett welcomed the ruling.

''This is the end of so-called 'scientific' whaling, surely,'' Mr Garrett told Fairfax Media. ''It's an incredible result. The comprehensive nature of it, and the way the court has taken on board our arguments.''

Shadow attorney-general Mark Dreyfus said he was "thrilled" at the court's "pioneering" decision. As Attorney-General when Labor was in government, Mr Dreyfus led Australia's legal challenge to Japan's "scientific" whaling program at the International Court of Justice in The Hague.

Mr Dreyfus told ABC radio on Tuesday he was optimistic that Japan, as a "fine international citizen", would abide by the court's ruling.

The court's decision could also have wider impacts on other whaling countries, he suggested.

"This decision . . . can't but have some effect on whaling in other parts of the world," Mr Dreyfus said. "It will add to pressure on . . . those small number of countries who continue to engage in whaling."

Sea Shepherd Australia Managing Director Jeff Hanson said the court decision vindicated Sea Shepherd for not only upholding Australian federal laws but also international laws in defending the Southern Ocean Whale Sanctuary ''for the whales and for future generations''.

''In the absence of law enforcement in the Southern Ocean, Sea Shepherd has been the only organisation upholding the law in defence of the International Whale Sanctuary,'' he said in a statement.

Greenpeace Oceans campaigner Nathaniel Pelle said the ruling confirmed Japan's whaling program was an ''illegal and unnecessary hunt of protected species'' and it was high time the industry was ''consigned to the history books''.

Prominent Australians welcomed the ICJ's decision.

A whale of a win! Paul Watson is a global hero and Australians can all feel proud. — Bob Brown (@BobBrownFndn) March 31, 2014

This is a truly historic decision & vindicates the decision our action. It means that so called scientific whaling is no more! — Peter Garrett (@pgarrett) March 31, 2014

Great news upholding Australia's case against whaling in International Court of Justice-proud of decision of Labor Govt to take legal action — Anthony Albanese (@AlboMP) March 31, 2014

Case launched in 2010

Australia sought an order from the International Court of Justice to stop the Japanese whale hunt in a case launched by the Rudd government in 2010.

The case began as tortuous diplomatic negotiations for Japan to phase out its Antarctic hunt broke down in the International Whaling Commission.

Other anti-whaling nations, including the United States, warned Australia against going to the court to fight the hunt which kills hundreds of whales each summer.

Then oppostion leader Tony Abbott also rejected the legal bid to end whaling, despite his then environment spokesman Greg Hunt urging the government to submit court documents.

He said while the Coalition would like Japan to stop whaling, ''we don't want to needlessly antagonise our most important trading partner, a fellow democracy, an ally''.

Washington's IWC Commissioner, Monica Medina, said that it was an uncertain gamble on whales' lives.

"This is a 'bet-the-whales' case," Ms Medina said then.

But a series of opinions by legal expert panels gathered by international wildlife conservation groups encouraged the then environment minister, Peter Garrett.

He argued strongly inside the Rudd government for taking on Japan, WikiLeaks documents showed.

When the case came to hearing in the Hague last June, it hinged on the court's view of the IWC convention's clause letting any member nation conduct its own scientific whaling program, despite a global moratorium on commercial whaling.

The Australian government's counsel, Bill Campbell, QC, told the 21 judges they had an important opportunity to decide for the world what did, and did not, constitute scientific activity.

"In short, Japan seeks to cloak its ongoing commercial whaling in the lab coat of science," Mr Campbell said.

"It simply is not science."

Japan currently issues its fleet with a scientific permit for a quota of up to 935 minke whales, 50 fin whales and 50 humpbacks, with the humpback quota currently "suspended".

Then attorney-general Mark Dreyfus said the case was not about an Australian "civilising mission" against Japan.

"This case is about one country's failure to comply with its legal obligations not to conduct commercial whaling," Mr Dreyfus said.

Japan claimed a clear and indisputable right under the convention to conduct its scientific program.

"Australia has pursued an express policy of using the IWC, against its stated purpose, to ban all whaling," Japan's counsel, Payam Akhavan, said.

"It has politicised science in order to impose Australian values on Japan in disregard for international law," Mr Akhavan said.

The decision comes with the whaling fleet under increased pressure from conservationist direct action that brought serious conflict to the far south - much of it in waters off the Australian Antarctic Territory.

However, despite this pressure from Greenpeace and Sea Shepherd, the whalers killed 10,439 minkes and 15 fin whales under scientific permit from the 1986 moratorium until the end of the 2013 season, according to the International Fund for Animal Welfare.

Last season's kill figure has not yet been released.

Established in 1945, the ICJ is the UN's highest judicial body and the only one of five principal UN bodies not located in New York.

The ICJ's judgements are binding and cannot be appealed.

- with AFP and James Massola