Japan, which says most whale species are not endangered and that eating whale is part of its culture, has long campaigned without success for the IWC to allow commercial whaling.
It reverses decades of policy as the commission issued an global suspension of commercial hunting in 1986 but Japan has since been whale hunting in the name of scientific research, with much of the meat also ending up on store shelves.
The decision by Tokyo to withdraw from the International Whaling Commission (IWC), which regulates whaling and has banned it, after 57 years as a member was criticised by allies and conservation groups.
Activist groups slammed the decision, with Greenpeace calling it a "sneaky" announcement.
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The IWC imposed the moratorium on commercial whaling three decades ago due to a dwindling whale population.
"We continue to hope Japan eventually reconsiders its position and will cease all whaling", he said.
"Commercial whaling. will be limited to Japan's territorial waters and exclusive economic zones".
Amy Laurenson, the acting New Zealand Whaling Commissioner said under the worldwide law of an exclusive economic zone, Japan could hunt for whales in an area that extends up to 200 nautical miles of the country.
"This is a grave mistake which is out of step with the rest of the world", said Sam Annesley, executive director at Greenpeace Japan. It's a fraction of the country's whale meat supply of about 200,000 tons before the IWC moratorium.
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Tempers frayed and police with batons fired tear gas to repel a few demonstrators trying to break through the officers' line. Ten people have died in incidents linked to the demonstrations, mostly in accidents at roadblocks set up by the protesters.
"Once commercial whaling resumes, I believe supply (of whale meat) will stabilize", he said. It had argued a "sustainable whaling committee" should be established, and that there were enough of some types of whale to allow for sustainable hunting, The Guardian reported.
In the 1950s, the practice reached its peak amid growing demand for whale meat as a key source of protein in the years following World War II, when the nation was poor and recovering from the devastation.
"Australia remains resolutely opposed to all forms of commercial and so-called "scientific" whaling", its environment minister, Melissa Price, and foreign minister, Marise Payne, said in a statement. This includes 372 minke whales, 26 Bryde's whales, and 90 sei whales.
Kazutaka Sangen, mayor of Taiji, a central Japanese town known for dolphin hunts, welcomed the decision and vowed to stick with scientific way of stock management so that Japan's position on whaling can gain understanding from the worldwide community.
In 2014, the International Court of Justice ordered it to halt its whaling programme in the Southern Ocean, also called the Antarctic Ocean, after determining that the hunting permits granted by authorities were not being used "for purposes of scientific research". Fisheries officials say that whale meat is more popular with older segments of the Japanese population than among the young.
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