Three ships have left Shimonoseki, Yamaguchi Prefecture, to join the mother vessel Nisshin Maru and hunt up to 935 Antarctic minke whales and 50 fin whales through March.
The Fisheries Agency had kept secret the departure date of the whaling fleet as a precaution against obstruction by the anti-whaling group Sea Shepherd Conservation Society, whose activities are expected to be monitored by a Japanese surveillance ship.
During the last season, the whalers killed 103 Antarctic minke whales, the smallest catch since Japan began what it calls "research whaling" in 1987, due to Sea Shepherd's activities and bad weather.
Environmentalists have condemned Japan's annual hunts in the Antarctic Ocean as a cover for commercial whaling.