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Japan catches about 1,000 whales each year for what it calls scientific research. Australia filed a case with the ICJ in May 2010, arguing that Japan's programme - under which it kills whales - is commercial whaling in disguise.
The court's decision is considered legally binding. Japan had said earlier that it would abide by the court's ruling.
Reading out the judgement on Monday, Presiding Judge Peter Tomka ordered a temporary halt to the programme.
The court said it had decided, by 12 votes to four, "that Japan shall revoke any extant authorisation, permit or licence granted in relation to JARPA II [Japan's whaling programme in the Antarctic] and refrain from granting any further permits in pursuance of that programme," BBC reported.
In a statement, the court said that Japan's programme involved activities which "can broadly be characterised as scientific research".
However, it said that "the evidence does not establish that the programme's design and implementation are reasonable in relation to achieving its stated objectives."
It added: "The court concludes that the special permits granted by Japan for the killing, taking and treating of whales in connection with JARPA II are not 'for purposes of scientific research' pursuant to [the International Convention for the Regulation of Whaling]."