Shinzo Abe's comments put him firmly on a collision course with anti-whaling groups, who had hoped the ruling by the International Court of Justice (ICJ) would herald the beginning of the end for the mammal hunt.
"I want to aim for the resumption of commercial whaling by conducting whaling research in order to obtain scientific data indispensable for the management of whale resources," Abe told a parliamentary commission.
"To that end, I will step up efforts further to get understanding from the international community," he said.
"It is regrettable that this part of Japanese culture is not understood," Abe said.
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Japan has hunted whales under a loophole in the 1986 global moratorium, which allows lethal research on the mammals, but it has made no secret of the fact that their meat ends up in restaurants and on fish markets.
The annual hunt in the Southern Ocean has proved particularly controversial, with sometimes violent confrontations between whalers and protesters.
The court slammed the hunt, which it said was a commercial venture masquerading as research.
Tokyo called off its 2014-15 Antarctic season, and said it would redesign the mission in a bid to make it more scientific.
A separate hunt in the northwest Pacific continues, as do hunts in coastal waters which are not covered by the moratorium.
Since the ICJ ruling, Japanese e-commerce marketplace Rakuten has told online retailers they cannot sell whale and dolphin meat through.