Two Japanese whaling ships and a surveillance vessel left Saturday for the annual hunt in the Antarctic Sea, Kyodo News said.
The three ships departed from the western port of Shimonoseki to join other ships to hunt up to 935 Antarctic minke whales and up to 50 fin whales through March, the news agency said.
The Fisheries Agency had kept secret the departure date of the whaling fleet as a precaution against obstruction by militant antiwhaling groups such as Sea Shepherd, Kyodo said.
Japan's whale hunts have long drawn criticism from activists and foreign governments, but Tokyo defends the practice saying eating whale is part of Japanese culinary tradition.
Japan says whales are studied as part of a bid by its whaling research institute to prove their populations can sustain commercial whaling.
Activists charge Tokyo's "research whaling" is cover for commercial whaling that is banned under an international agreement.
Japanese whalers and Sea Shepherd activists have routinely clashed violently in exchanges that have seen stink bombs thrown at Japanese crew and water jets trained on protesters.
Japan's whaling catch fell to a record low of 103 Antarctic minke whales in the last season due mainly to the antiwhaling group.