Japan chose to withdraw from the organization since its calls for the whaling resumption due to the growing number of whales had not been supported by other states in the IWC, the NHK World broadcaster reported.
Reports of the impending decision - an unusual step for Japan, which stresses multilateralism in its diplomacy - had sparked criticism from global conservationist groups. A proposal to allow the commercial hunt of minke whales and other species which Japan believes are "relatively abundant" was recently rejected.
The move on Wednesday, which is expected to draw worldwide criticism, came more than three months after the global body for the conservation of whales rejected a Tokyo-led proposal to lift a 32-year ban on the commercial hunting of the mammals.
Japanese whaling towns Wednesday welcomed the government's decision to withdraw from the International Whaling Commission, but some local residents voiced concern that it may lead to an escalation in protests.
"We will not hunt in the Antarctic waters or in the southern hemisphere", he added.
The IWC imposed the moratorium on commercial whaling three decades ago due to a dwindling whale population.
Leaving the IWC means Japanese whalers will be able to resume hunting in Japanese coastal waters of minke and other whales now protected by the IWC.
Last season, its scientific research expeditions caught almost 600 whales in the Antarctic and the northwest Pacific.
But Japan will not be able to continue the so-called scientific research hunts in the Antarctic that has been exceptionally allowed as an IWC member under the Antarctic Treaty.
Japan has hunted whales for centuries, and the meat was a key source of protein in the immediate post-World War II years when the country was desperately poor.
Paul Watson, the founder of the anti-whaling activist group Sea Shepherd, also said in a statement that Japan would be declaring itself "a pirate whaling nation" by withdrawing from the IWC.
"The declaration today is out of step with the global community, let alone the protection needed to safeguard the future of our oceans and these majestic creatures", said Sam Annesley, executive director at Greenpeace Japan.
Some influential lawmakers' constituencies include whaling communities, and Prime Minister Shinzo Abe's election district is home to the whaling port of Shimonoseki.
By the way, today's announcement doesn't mean that Japan hasn't been hunting whales all this time.
However, Japan's conservative government argues that there is a need to pass whaling culture on to the next generation. Fisheries officials say that whale meat is more popular with older segments of the Japanese population than among the young.