Japan announced on December 26 that it will leave the International Whaling Commission (IWC) at the end of June and resume commercial whaling in July for the first time in about 30 years.
Mr Suga said: "At the IWC general meeting in September this year it became evident once again that those supporting the sustainable use of whale stocks and those supporting protection can not co-exist, leading us to this conclusion".
The withdrawal from the IWC may be a face-saving step to stop Japan's ambitious Antarctic hunts and scale down the scope of whaling to around the Japanese coasts.
Tokyo has repeatedly threatened to pull out of the IWC, 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.
The withdrawal means Japan joins Iceland and Norway in openly defying the IWC's ban on commercial whale hunting.
"But if we don't explain internationally that whales are increasing. people won't understand", she added.
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.
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.
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While this is a benefit for the Antarctic, it may simply be because the nation is no longer able to hunt on the high seas, where they were claiming to be conducting "scientific whaling" while still a member of the IWC.
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.
Japan has hunted whales for centuries but has subdued its catch following global protests and diminishing demand for whale meat at home.
Tokyo maintains most whale species are not endangered, and eating whale meat is part of its culture.
"It's clear that the government is trying to sneak in this announcement at the end of year, away from the spotlight of worldwide media", said Sam Annesley, the Executive Director at Greenpeace Japan.
Abe's own electoral district includes Shimonoseki, a whaling port in western Japan.
The resumption of commercial whaling is an unusual decision for Japan, which stresses multilateralism in its diplomacy, and it sparked swift criticism from environmental groups and others who believe all whales should be protected.
It makes no secret however of the fact that meat from the expeditions ends up on dinner tables.
Japan has cut back on its catch as Japanese consume less whale meat.