thumb|upright=1.35|A whale and a sub-adult being loaded aboard a [[factory ship, the Nisshin Maru. The sign above the slipway reads, "Legal research under the ICRW." Australia released this photo to challenge that claim.]]

Japanese whaling, in terms of active hunting of whales, is estimated by the Japan Whaling Association to have begun around the 12th century. However, Japanese whaling on an industrial scale began around the 1890s when Japan started to participate in the modern whaling industry, at that time an industry in which many countries participated.

During the 20th century, Japan was heavily involved in commercial whaling. This continued until the International Whaling Commission (IWC) moratorium on commercial whaling went into effect in 1986. Japan continued to hunt whales using the scientific research provision in the agreement, and Japanese whaling was conducted by the Institute of Cetacean Research. This was allowed under IWC rules, although most IWC members opposed it. However, in March 2014, the UN's International Court of Justice ruled that the Japanese whaling program called "JARPA II" in the Southern Ocean, including inside the Australian Whale Sanctuary, was not in accordance with the International Convention for the Regulation of Whaling, and was not for scientific purposes, as it had claimed. They ordered Japan to cease operations. In response to the ruling, Japan formulated a new Antarctic research whaling program, "NEWREP-A", to replace JARPA II. Under this program, 333 Antarctic minke whales were hunted each year from 2015 to 2018. On 1 July 2019, Japan withdrew from the IWC and resumed commercial whaling, claiming that the IWC's original goal of sustainable whaling had been lost. As a result, Japanese whaling will now only take place in Japan's territorial waters and exclusive economic zones, moving away from the high seas in order to avoid trade violations under CITES. In 2024, Japan hunted 179 Bryde's whales, 87 minke whales, 30 fin whales, and 25 sei whales.

Antarctic hunts were a source of conflict between pro- and anti-whaling countries and organizations. Antarctic minke whales abundance in the East Antarctic Ocean may have remained stable or declined slightly during JARPA, but this is thought to be due to a decline in krill as a result of the increase in humpback whales. The International Union for Conservation of Nature (IUCN), on the other hand, listed it as Near Threatened (NT) in 2018. The UN's International Court of Justice, in addition to other countries, scientists, and environmental organizations, consider the Japanese research program to be unnecessary and lacking scientific merit, and describe it as a thinly disguised commercial whaling operation. Japan, echoing Norway's arguments on its own whaling activities, also argues it is entitled to continue whaling because of whaling's place in its cultural heritage. The whale meat from these hunts is sold in shops and restaurants, and is showcased at an annual food festival that, in some cases, features the butchering of a whale for onlookers. A poll in 2014 found that few Japanese people have been eating whale meat regularly since whale-based dishes disappeared from school lunches in 1987. Surviving Ainu folklore reveals a long history of whaling The earliest records of hand-thrown harpoons date from the 12th century.

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Organized whaling

thumb|Illustrations of the whaling techniques of Taiji, Japan, in 1857

Organized open-boat shore whaling began in the 1570s, and continued into the early 20th century. Techniques were developed in the 17th century in Taiji, Wakayama. Wada Chubei Yorimoto established a fishery by organizing the group hunting system in 1606. Whalers would spot whales from stations along the shore and launch boats to catch them with harpoons and lances. His grandson, Wada Kakuemon Yoriharu, later known as Taiji Kakuemon Yoriharu, invented the whaling net technique called amitori-shiki (網取り式).

Primarily right whales, humpback whales, gray, and fin whales were hunted.

Domestically, Japanese writers have tried to call attention to historical whale declines due to whaling practices by other nations over hundreds of years, some of which continue today, and assert that motives and objectives of Japanese whaling customs differ from other nations. Supporters of the Japanese whaling tradition claim that the experience is both humble and emotional, and all parts of a whale are used, unlike westerners of the past who hunted only for whale oil. In addition, Japan has strictly controlled catch quotas, and whalers have never hunted juveniles or cow/calf pairs due to their respect for whales. When they kill whales, hunters invoke the Buddha and pray for the repose of whales' souls;

Even though Buddhists were opposed to hunting whales, due to the whales' great care for their calves, enforcement of the Shorui-Awaremi-no-rei (ordinances of animal protection) excluded whales due to being perceived locally as fish, despite the fulfillment of terms of protection for having "mammalian natures", and that a paper regarding whales as mammals was published in Kyoto in 1758. As a precept, Buddhists and other concerned people created folklore tales about whaling communities and those who practiced whaling on an industrial scales met tragic downfalls by supernatural phenomenon such as phantoms and the curses of whales.

North Pacific right whales followed by grays and humpbacks were considered to be the primary targets, and the industries were devastating to the stocks as catch quantities had been reduced dramatically in relatively short periods. The effect of the industries were more notable on the whale populations than the later American whaling. This decline of coastal stocks resulted not only in financial solvency of many industrial groups but also in disputes between feudal domains in western Japan that required the intervention of the shogunate. As early as the Edo period, Japanese writers may have tried to call attention to overkill by American and Norwegian whalers, whose hunting practices led to depletion of whale populations, and the tragedy called Semi-nagare, an incident in which over 100 Taiji whalers were lost in the ill-timed pursuit of the only two whales they had seen in December 1878. The incident effectively marked the end of traditional Japanese whaling practice.

Some areas of Japan did not whale and opposed whaling, in particular in Northeast Japan where Japanese fishermen believed that whales were an incarnation of the god Ebisu.

Modernization

The modernization of Japanese whaling began with the adaptation of Western whaling methods around 1860. In 1861, the Tokugawa shogunate dispatched Nakahama Manjirō to the Bonin Islands on a Western-style schooner to practice whaling in the manner of the Western or "Yankee" whalers that were active in the West Pacific at that time. From whalers that had settled in the Bonin Islands, Manjirō purchased new tools such as the bomb lance, an explosive projectile that was used in whaling.

Norwegian-style modern whaling, based on the use of power-driven vessels, cannons and exploding harpoons, was introduced in the Meiji period largely through the efforts of Jūrō Oka who is considered the "father of modern Japanese whaling". Oka traveled the world gathering information about whaling practices including to Norway for harpoons, cannons and expertise. He also established the first modern whaling company in Japan in 1899, Nihon Enyo Gyogyo K.K. which took its first whale on February 4, 1900, with a Norwegian gunner, Morten Pedersen.

In the early 20th century, Jūrō Oka dominated the whale meat market in Japan with assistance and instruction from Norwegian whalers and their leased or purchased ships. Another boost was provided by the capture of a Russian whaling fleet and subsequent transfer to Toyo GyoGyo Co. Ltd. As imperial Japan's whaling industry expanded into the new territory opened up by their colonization of Korea and Taiwan, Oka's company (renamed Toyo Hogei K.K.) returned significant profits to its investors which led to increased Japanese competition. Oka later became the first president of the Japan Whaling and Fishing Association, established in 1908.