When the commercial whaling moratorium was introduced by the IWC in 1982, Japan lodged an official objection. However, in response to US threats to cut Japan's fishing quota in US territorial waters under the terms of the Packwood-Magnuson Amendment, Japan withdrew its objection in 1987. According to the BBC, America went back on this promise, effectively destroying the deal. Since Japan could not resume commercial whaling, it began whaling on a purported scientific-research basis. Australia, Greenpeace, the Sea Shepherd Conservation Society and other groups dispute the Japanese claim of research “as a disguise for commercial whaling, which is banned.” The Sea Shepherd Conservation Society has attempted to disrupt Japanese whaling in the Antarctic since 2003.

The stated purpose of the research program is to establish the size and dynamics of whale populations. The Japanese government wishes to resume whaling in a sustainable manner under the oversight of the IWC, both for whale products (meat, etc.) and to help preserve fishing resources by culling whales. Anti-whaling organizations claim that the research program is a front for commercial whaling, that the sample size is needlessly large and that equivalent information can be obtained by non-lethal means, for example by studying samples of whale tissue (such as skin) or feces. The Japanese government sponsored Institute of Cetacean Research (ICR), which conducts the research, disagrees, stating that the information obtainable from tissue and/or feces samples is insufficient and that the sample size is necessary in order to be representative.

Japan's scientific whaling program is controversial in anti-whaling countries. Countries opposed to whaling have passed non-binding resolutions in the IWC urging Japan to stop the program. Japan claims that whale stocks for some species are sufficiently large to sustain commercial hunting and blame filibustering by the anti-whaling side for the continuation of scientific whaling. Deputy whaling commissioner, Joji Morishita, told BBC News:

This collusive relationship between the whaling industry and the Japanese government is sometimes criticized by pro-whaling activists who support local, small-scale coastal whaling such as the Taiji dolphin drive hunt.

On 26 December 2018, Japan announced that since the IWC failed its duty to promote sustainable hunting, which is one of its stated goals, Japan is withdrawing its membership. Japanese officials also announced they will resume commercial hunting within its territorial waters and its 200-mile exclusive economic zones starting in July 2019, but it will cease whaling activities in the Antarctic Ocean, the northwest Pacific ocean, and the Australian Whale Sanctuary.
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