The research programme has been criticised as a cover for commercial hunting as the meat is sold on the market at home.
Commercial whaling was banned under a 1986 International Whaling Commission moratorium.
The environmental group Greenpeace condemned Wednesday's announcement and disputed Japan's view that whale stocks have recovered, and noted that ocean life is being threatened by pollution as well as overfishing.
"It's clear that the government is trying to sneak in this announcement at the end of year, away from the spotlight of global media", said Sam Annesley, the Executive Director at Greenpeace Japan.
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.
New Zealand's foreign affairs minister Winston Peters also had his say on the issue, saying that he was "disappointed" with the move, adding: "Whaling is an outdated and unnecessary practice".
Two countries including Canada and Iceland have withdrawn from the global bod, with the latter re-joining in 2003 after leaving in 1992.
The IWC imposed a commercial moratorium in the 1980s due to a dwindling whale population.
It was not yet clear how many whales would be caught each year once Japan resumes commercial whaling, officials said.
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By leaving the IWC, Japan steps back from the body's founding document, the International Convention for the Regulation of Whaling, which was signed in 1946.
"It's not like we are turning our back on the IWC and abandoning worldwide cooperation", she said.
A number of coastal communities in Japan have hunted whales for centuries, but consumption in the country surged only after World War II.
She added: "This is the path of a pirate whaling nation, with a troubling disregard for global rule".
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 Fisheries Agency said Japan plans to catch three kinds of whale that are believed to have sufficient stocks - minke, sei and Bryde's.
Reports of the impending decision - an unusual step for Japan, which stresses multilateralism in its diplomacy - had sparked criticism from worldwide conservationist groups.
As a result, Japan will stop hunting in Antarctic waters and the southern hemisphere, a prospect conservation groups had welcomed before it was formally confirmed.
A 73-year-old woman was hopeful that the resumption of commercial whaling would lead to the revival of Taiji, but said she fears "violent anti-whaling activities could increase" in the future.