Two Fisheries Agency ships left for the Antarctic Ocean on Thursday to survey whale stocks in place of an annual cull that the International Court of Justice halted last year.
The fleet departed from Shimonoseki port in Yamaguchi Prefecture on Thursday.
Through March, scientists will record visual contacts and take samples of whale skin, but won't catch the animals. Whaling guns have been removed.
Japan has vowed to resume "research whaling" in 2015 and submitted to the International Whaling Commission a revised plan that limits the hunt to minke whales and cuts the cull size by two-thirds to 333.