Australia, one of Japan's biggest critics on the issue, said it was "extremely disappointed".
"Their decision to withdraw is regrettable and Australia urges Japan to return to the commission as a matter of priority," the federal government said in a statement on Wednesday.
"Australia remains resolutely opposed to all forms of commercial and so-called 'scientific' whaling.
"We will continue to work within the commission to uphold the global moratorium on commercial whaling."
The government said the decision not to hunt in the Southern Ocean, where Australia provides protection, would ensure the Antarctic "will finally be true sanctuaries for all whales".
The IWC, which imposed a commercial moratorium in the 1980s due to a dwindling whale population, rejected Tokyo's request to resume commercial whaling in September.
Japan has claimed stocks have recovered enough to resume commercial hunting.
It has been accused of conducting commercial whaling under the guise of scientific research and has been estimated to kill 450 whales annually.
The announcement has angered conservationists.
"Japan now becomes a pirate whaling nation killing these ocean leviathans completely outside the bounds of international law," Humane Society International president Kitty Block said.