A fleet of four whaling ships left Ayukawa port in the city of Ishinomaki, 340km north-east of Tokyo, for their seasonal hunt with the whalers aiming to catch up to 60 minke whales through June, the Kyodo News agency reported.
They will dissect the whales caught and analyse their gastric samples to research the mammals' impact on the marine ecosystem, Kyodo said.
The whaling is conducted by the Association for Community-based Whaling, which is based in Fukuoka, southern Japan.
Yoshiichi Shimomichi, who leads the group, was quoted by Kyodo as saying it "aims to resume Japan's traditional whaling in coastal waters."
Researchers will check radiation levels in whale meat in the wake of Japan's worst nuclear disaster at the Fukushima Daiichi Nuclear Power Station, caused by the March 2011 earthquake and tsunami.
Japan officially halted commercial whaling in 1987 in response to the previous year's moratorium. The country has used a loophole to continue whaling under the premise of scientific research despite international opposition.
Most Japanese do not eat whale meat, but vested interests keep whaling going, critics said.