Japan has claimed stocks have recovered enough to resume commercial hunting.
The Sankei newspaper said the decision was made at a cabinet meeting on Tuesday after the government decided it would be hard to resume commercial whaling while a member of the worldwide body.
Japan is to resume commercial whaling in July after withdrawing from the International Whaling Commission.
Japanese media said that Japan could no longer take advantage of the IWC exemption for scientific whaling if it withdrew from the group because the United Nations Convention on the Law of the Seas requires its signatories, including Japan, to work through "the appropriate global organizations" for marine mammal conservation.
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.
The announcement had been widely expected and comes after Japan failed in a bid earlier this year to convince the IWC to allow it to resume commercial whaling.
The research program was criticized as a cover for commercial hunting as the meat was still sold in stores.
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.
In the vote at that IWC meeting, 41 member countries opposed Japan's proposal to lift the IWC's moratorium on commercial whaling, while 27 members supported it, and two abstained.
Japan began scientific whaling in 1987, a year after an global whaling moratorium began.
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.
The decision to restart commercial whaling has sparked global criticism.
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.
"There have been no concessions from countries who only place importance on the protection of whales", Suga said.
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.
"This is a grave mistake which is out of step with the rest of the world", said Sam Annesley, executive director at Greenpeace Japan.
It makes no secret however of the fact that meat from the expeditions ends up on dinner tables.
"We would like to wholeheartedly celebrate an end to Japan's whaling in the Southern Ocean, but if Japan leaves the International Whaling Commission and continues killing whales in the North Pacific it will be operating completely outside the bounds of international law".