"But if we don't explain internationally that whales are increasing. people won't understand", she added.
Tokyo has repeatedly threatened to pull out of the body, and has been regularly criticised for catching hundreds of whales a year for "scientific research" despite being a signatory to a moratorium on hunting the animals.
"Regrettably, we have reached a decision that it is impossible in the IWC to seek the coexistence of states with different views", Mr Suga said.
Reports of the impending decision - an unusual step for Japan, which stresses multilateralism in its diplomacy - had sparked criticism from worldwide conservationist groups.
"Whaling is an outdated and unnecessary practice. We continue to hope Japan eventually reconsiders its position and will cease all whaling in order to advance the protection of the ocean's ecosystems", Peters said in a statement.
Japan has hunted whales for centuries, and the meat was a key source of protein in the immediate post-World War II years when the country was desperately poor.
But consumption has declined significantly in recent decades, with much of the population saying they rarely or never eat whale meat.
Japan began scientific whaling in 1987, a year after the global whaling moratorium began.
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Some influential lawmakers' constituencies include whaling communities, and Prime Minister Shinzo Abe's election district is home to the whaling port of Shimonoseki.
However, Japan's conservative government argues that there is a need to pass whaling culture on to the next generation.
Japan will resume commercial whaling in July 2019 after a 30-year absence "in line with Japan's basic policy of promoting sustainable use of aquatic living resources based on scientific evidence", he said.
By the way, today's announcement doesn't mean that Japan hasn't been hunting whales all this time.
In 2014, the International Court of Justice ordered it to halt its whaling programme in the Southern Ocean, also called the Antarctic Ocean, after determining that the hunting permits granted by authorities were not being used "for purposes of scientific research".
"The declaration today is out of step with the worldwide community, let alone the protection needed to safeguard the future of our oceans and these majestic creatures", Sam Annesley, executive director at Greenpeace Japan, said in a statement.
It reverses decades of policy as the commission issued an global suspension of commercial hunting in 1986 but Japan has since been whale hunting in the name of scientific research, with much of the meat also ending up on store shelves.
Japan is the biggest financial contributor to the IWC, which may now have to find ways to replace lost funding.
The move comes just months after the commission once again refused to allow Japan to hunt whales commercially.