The decision ignores a ban on trading in the animals, some of which were in danger of dying out.
But both countries say there's now plenty of minke whales in the world's oceans and hunting won't harm the overall population.
Whale meat in Norway costs about half of the price in Japan.
Japanese officials hope that by buying in cheap Norwegian meat more people will start eating it again.
Whale meat used to be common in Japanese school canteens but now it's rare and expensive.
But conservation groups are angry at the news.
They're worried the ban could one day be overturned completely.