The country has hunted minke whales under an exemption in the global ban on commercial whaling that allows the animals to be killed for research.
It makes no secret of the fact that meat from the mammals - killed ostensibly for science - is processed into food, claiming the whale population is big enough to allow sustainable whaling.
But it suspended its annual research expedition to the Antarctic Ocean last year after the United Nations' top legal body ruled that it was being used to skirt the moratorium.
Respecting the judgement, Japan sent whaling ships but they returned with no catch.
Earlier this year, Japan told the International Whaling Commission (IWC), which is responsible for setting catch limits for commercial whaling, that it will resume whaling by the end of March next year.
It said it will cut its annual minke whale catches by two-thirds to 333.
The IWC dismissed the proposal, saying that Japan had failed to explain in sufficient detail why it still needed to kill nearly 4,000 whales over the next 12 years.
But on Friday Japan's fisheries agency decided to go ahead with the planned restart to its expedition, claiming that it was scientifically adequate, according to local media reports.
The Yomiuri Shimbun and other media said Japanese whalers were expected to depart for the ocean possibly by the end of December. There was no immediate comment from the agency.
Australian environmentalists criticised the announcement, urging Prime Minister Malcolm Turnbull to stand up to Japan.
'The Australian government must step up and challenge the Japanese government's illegal whaling,' said Darren Kindleysides from the Australian Marine Conservation Society.
'Japan's Antarctic whaling has failed the test of international law, and the test of science, yet the hunt could resume within weeks.'Japan has hunted whales in the Southern Ocean under an exemption in the global whaling moratorium that allows for lethal research.
Japan accuses opponents of being emotional about whales and disregarding what it says is evidence to support its position.
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