The nation, which has long argued it should be allowed to hunt whales as their meat has cultural significance, says it will not return to whaling in Antarctica though, and will stick to its territorial and economic waters. Third, it will "cease the take of whales in the Antarctic Ocean/the Southern Hemisphere".
"Regrettably, we have reached a decision that it is impossible in the IWC to seek the coexistence of states with different views", Suga said.
"The next great thing about it is that if they leave the IWC, that means the Atlantic whale sanctuary will then go ahead because they've been voting against that for years".
But Japan will not be able to continue the so-called scientific research hunts in the Antarctic and elsewhere that it has been exceptionally allowed as an IWC member.
With its IWC exit, Japan now joins Iceland and Norway in openly defying the organization's ban on commercial whale hunting.
"Whaling is an outdated and unnecessary practice".
Despite the fact that Japan officially refrained from whaling for about 30 years, whale meat from time to time could be found in the country's supermarkets and restaurants.
Mr Suga said Japan will notify the IWC of its decision by 31 December and remains committed to worldwide cooperation on proper management of marine living resources even after its IWC withdrawal.
Many members of Prime Minister Shinzo Abe's conservative Liberal Democratic Party are supporters of whaling, and he himself comes from a constituency where whale hunting remains popular.
"There have been no concessions from countries who only place importance on the protection of whales", Suga said.
He added that Japan is disappointed that the IWC - which he said is dominated by conservationists - focuses on the protection of whale stocks even though the commission has a treaty mandate for both whale conservation and the development of the whaling industry.
A Japanese whaling ship leaves the port of Shimonoseki in Yamaguchi prefecture, western Japan to resume whale hunting in the Antarctic.
Environmental group Greenpeace condemned the decision and disputed Japan's view that whale stocks have recovered, saying that ocean life is being threatened by pollution as well as overfishing.
Suga said Japan will notify the IWC of its decision by December 31 and remains committed to global co-operation on proper management of marine living resources even after its IWC withdrawal.
Japan is the biggest financial contributor to the IWC, which may now have to find ways to replace lost funding.
Japan has defied global protests to conduct what it calls "scientific research whaling", having repeatedly said its ultimate goal is to whale commercially again.
It makes no secret however of the fact that meat from the expeditions ends up on dinner tables.
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