The IWC imposed the moratorium on commercial whaling three decades ago due to a dwindling whale population.
Japan suspended its hunt for one season to re-tool its whaling programme with measures such as cutting the number of whales and species targeted, but resumed hunting in the 2015-2016 season, capping its Antarctic catch with a quota of 333 whales annually.
Yoshihide Suga, a government spokesman, made the announcement at a press briefing in Tokyo today. "The government of Japan must urgently act to conserve marine ecosystems, rather than resume commercial whaling".
Japan will resume commercial whale-hunting next year for the first time since 1988, joining Iceland and Norway in defying a ban on the practice.
Global conservation group Sea Shepherd has long protested against Japan's whaling programme, often trailing its whaling ships in Antarctic waters.
"As a result of modern fleet technology, overfishing in both Japanese coastal waters and high seas areas has led to the depletion of many whale species", Greenpeace International said.
Hideki Moronuki, a senior official at the Fishery Agency, told reporters: "A withdrawal is not the best option, but it is a better option in order to achieve Japan's major objective of commercial whaling".
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Japan has hunted whales for centuries, and their meat was a key source of protein in the immediate post-World War II years when the country was desperately poor.
The announcement was not surprising, as it comes after the IWC declined Japan's request to allow its fishermen to hunt minke and other whales protected by the organization.
Japan will resume commercial whaling in July 2019 after a 30-year absence "in line with Japan's basic policy of promoting sustainable use of aquatic living resources based on scientific evidence", he said.
Saito said many residents in the district were looking forward to anticipated benefits linked to the industry's restart, saying it may increase employment, revive the industry and allow them to eat more whale meat.
Greenpeace Japan's executive director Sam Annesley said the decision was "out of step with the global community".
"This is devastating news for the whales and we can only hope that conservation-minded countries like the United Kingdom will take appropriate measures to respond to Japan's decision, including the threat of sanctions".
"There have been no concessions from countries who only place importance on the protection of whales", Suga said.
It makes no secret however of the fact that meat from the expeditions ends up on dinner tables. "Engagement in whaling has been supporting local communities, and thereby developed the life and culture of using whales".