"Japan shall revoke any existant authorisation, permit or licence granted in relation to JARPA II (research programme) and refrain from granting any further permits," said the International Court of Justice's Judge Peter Tomka.
Agreeing with Australia, which in 2010 hauled Japan before the Hague-based ICJ in a bid to end whale hunting in the Southern Ocean, Tomka said that "special permissions granted by Japan are not for purposes of scientific research."
While Norway and Iceland have commercial whaling programmes in spite of a 1986 International Whaling Commission (IWC) moratorium, Japan insisted its programme was scientific, while admitting that the resulting meat ended up on plates back home.
Tokyo was accused of exploiting a legal loophole in the 1986 ban on commercial whaling that allowed the practice to collect scientific data.
Also Read
Conservation groups voiced happiness at the ruling, which Japan said it would respect despite "deep disappointment".
"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," chief negotiator Koji Tsuruoka told reporters outside the United Nations' top court.
"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," Campbell said.
Australia said that since 1988 Japan has slaughtered more than 10,000 whales under the programme, putting the Asian nation in breach of international conventions and its obligation to preserve marine mammals and their environment.
Pete Bethune, a former activist with militant conservation group Sea Shepherd who spent five months in a Japanese prison for his protests, broke down after the verdict.