The Japanese whaling fleet that left the northeastern fishing town of Ayukawa in April completed its mission last week, the Fisheries Agency said.
It was the first campaign since the International Court of Justice (ICJ) said in March that Japan's annual expedition to the Southern Ocean was a commercial activity masquerading as research.
The hunt, which takes place in spring and autumn in coastal waters and in the northwestern Pacific is also classified as "research whaling", but was not at issue in the ICJ case, which only addressed the Southern Ocean hunt.
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.
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Tokyo called off the 2014-15 season for its Antarctic hunt, and said it would redesign the controversial whaling mission in a bid to make it more scientific.
Prime Minister Shinzo Abe sparked fury in anti-whaling nations earlier this month when he told parliament he would boost his efforts towards restarting commercial whaling.
Critics point out that while whale meat was once an important source of protein, few Japanese now eat it, despite government subsidies.
However, a recent poll by a major national newspaper found a majority of those questioned supported Japan's right to hunt the mammals.
Observers say the tactics of anti-hunt groups like Sea Shepherd, whose boats have harassed whalers in the Southern Ocean, has galvanised support among the population, where demands for an end to the mission are sometimes painted as cultural imperialism.