Japan is "deeply disappointed" that the UN's top court has ruled in favour of Australia by declaring its Southern Ocean whale hunt illegal, but nevertheless insists it will abide by the decision.
The International Court of Justice (ICJ) on Monday demanded Japan cease its whaling program "with immediate effect" as it didn't comply with the country's obligations under the international whaling convention.
The court agreed with Australia's long-held view that Japan's JARPA II research program wasn't "for purposes of scientific research" as allowed under Article 8 of the 1946 convention.
The Australian government welcomed the historic win, but stressed it would have no effect on diplomatic and trade ties with Japan.
Tokyo's agent at the ICJ, Koji Tsuruoka, addressed the world's media at the Peace Palace in The Hague after the judgment.
"Japan regrets and is deeply disappointed that JARPA II ... has been ruled by the court as not falling within the provisions of Article 8," he told reporters.
"However, as a state that respects the rule of law, the order of international law and as a responsible member of the global community, Japan will abide by the decision of the court."
Mr Tsuruoka refused to discuss whether Japan would design a new research program in the hope of resuming whaling at a later date.
He said Japan would digest the complex judgment before officials would "be able to consider what future course of action we should take".
Australia's agent, Bill Campbell QC, welcomed the decision, but emphasised differences over whaling wouldn't impact on the overall bilateral relationship between Canberra and Tokyo.
"The decision of the court today, important as it is, has given us the opportunity to draw a line under the legal dispute and move on," Mr Campbell said.
Monday's judgment comes seven years after then-opposition leader Kevin Rudd first pledged a future Labor government would take legal action against Tokyo.
Rudd was duly elected prime minister in November 2007, but it took another 18 months before the government instituted proceedings in mid-2010.
Current Labor deputy leader Tanya Plibersek said Monday's ruling meant a program which saw thousands of whales killed in Antarctic waters had at last been ended.
"The (coalition) government should now take up discussions with Japan to co-operate on genuine and non-lethal methods of whaling research," she said.
The court criticised Japan for not focusing more on research methods that didn't involve killing whales.
Prime Minister Tony Abbott travels to Japan in early April and will meet with his counterpart, Shinzo Abe, in an attempt to finalise a free trade agreement.
A Japanese delegation spokesman in The Hague told AAP it wasn't yet known if the pair would discuss whaling.
"But we are thinking Mr Abbott's visit to Japan is with a view to strengthening our ties," Noriyuki Shikata said.
Australia had argued before the 16-judge ICJ panel that Tokyo was cloaking a commercial whaling operation "in the lab coat of science" despite agreeing to a 1980s ban on harpooning.
Japan, however, countered during a three-week hearing in mid-2013 that the court didn't have the authority to decide what was, or wasn't, science.
But the court on Monday dismissed Tokyo's argument.
President Judge Peter Tomka ruled: "The evidence does not establish that the (whaling) program's design and implementation are reasonable in relation to its stated (scientific) objectives."