Commercial whale hunting is banned in South Korea, but the trading of whales found dead is still legal, the BBC reported Tuesday.
Critics have alleged fishermen were exploiting the loophole in the law.
Under the new rules, fishermen will be required to report to police immediately if they discover dead whales in their nets or washed ashore.
The new regulations require samples from all dead whales be given to authorities for testing, and their meat can only be sold after a full investigation into how the animal died.
Fishermen who obtain dead whales, either at sea or ashore, will only be allowed to process and sell them at state-designated facilities, South Korea's Agricultural Ministry said.
Commercial whaling was banned in South Korea when the International Whaling Commission implemented a global moratorium in 1986.