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.

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.

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.

- The Age