A fleet of four Japanese ships left the northern main island of Hokkaido on Sunday to start the seasonal "research" whaling hunt in Pacific coastal waters, local media said.
Japan's Fisheries Agency has said whalers planned to kill up to 51 minke whales in waters off Kushiro city through the end of October.
Japan has hunted whales under a loophole in the 1986 global moratorium that allows lethal research on the mammals, but has made no secret of the fact that their meat ends up in restaurants and fish markets.
Agency officials could not be immediately reached on Sunday.
The smaller scale Pacific coastal whaling comes as Japan hopes to resume its Antarctic Ocean hunt next year, despite an order from the UN's top court to stop all whaling in the area.
Tokyo was forced to abandon its 2014-15 hunt in March when the International Court of Justice (ICJ) said the annual expedition was a commercial activity masquerading as research.
But the pro-whaling government hopes to bypass this ruling by giving the controversial mission a more scientific focus.
The latest expedition, officially to survey the contents of whales' stomachs, is one of the few hunts not covered by the ICJ ruling.
One in July saw the slaughter of 90 sei whales and 25 Bryde's whales, while in another through June some 30 minke whales were killed as part of a coastal hunt.