The country announced the plan on Wednesday, abandoning a decades-old campaign to persuade the commission to allow it to hunt whales commercially.
Japan’s commercial whaling will be limited to its own territorial waters and its exclusive economic zone, said Chief Cabinet Secretary Yoshihide Suga, who made the announcement at a news conference after a cabinet decision on Tuesday.
"From July 2019, after the withdrawal comes into effect on June 30, Japan will conduct commercial whaling within Japan’s territorial sea and its exclusive economic zone, and will cease the take of whales in the Antarctic Ocean/the Southern Hemisphere," Suga said in a statement.
"The whaling will be conducted in accordance with international law and within the catch limits calculated in accordance with the method adopted by the IWC to avoid negative impact on cetacean resources," he said.
Japan’s decision followed the IWC’s latest rejection of its bid to resume commercial whaling at a September meeting, which Suga said showed it was impossible to bridge the gap between whaling advocates and anti-whaling members.
Reports of the impending decision - an unusual step for Japan, which stresses multilateralism in its diplomacy - had sparked criticism from international conservationist groups.
Japan has defied the protests to conduct what it calls scientific research whaling, having repeatedly said its ultimate goal was to whale commercially again.
In 2014, the International Court of Justice ruled that Japan should halt its Antarctic whaling.
Japan suspended its hunt for one season to re-tool its whaling program 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.
Japan has long maintained that most whale species are not endangered and that eating whale is part of its culture.
It began scientific whaling in 1987, a year after an international whaling moratorium began.
Much of the meat ends up on store shelves, even though most Japanese no longer eat it. Whale consumption accounted for 0.1 percent of all Japanese meat consumption, according to the Asahi newspaper.
Influential lawmakers in Prime Minister Shinzo Abe’s Liberal Democratic Party whose constituencies include whaling communities have long lobbied for a resumption of commercial whaling.
Abe’s own electoral district includes Shimonoseki, a whaling port in western Japan.