"The Nisshin Maru and two other whaling ships arrived here today after ending their mission," a port official said, following the fleet's planned arrival at Shimonoseki port in western Japan.
Television footage showed workers unloading a number of boxes labelled as whale meat parts at the port, marking the end of the traditional whaling season.
On Thursday, Japan said it was cancelling its next annual Antarctic whaling hunt, due to begin late 2014, for the first time in a quarter-century.
During the four-month voyage, the harpoon fleet faced its annual confrontation with environmental activist group Sea Shepherd in the Antarctic Sea.
Australia, backed by New Zealand, hauled Japan before the ICJ in 2010 in a bid to end the annual Southern Ocean hunt.
Tokyo has used a legal loophole in the 1986 whaling ban that allowed it to continue slaughtering the mammals, ostensibly so it could gather scientific data.
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