The missile was launched early on Tuesday Korean time, and it flew over Hokkaido Island before crashing into the sea.
The action marked the first time that the North would fire what is thought to be a ballistic weapon over Japan, despite a flurry of missile test that were conducted recently.
The Japanese Prime Minister SHINZO ABE has condemned the action, which he described as an unprecedented threat to his country.
Following the development; the United Nations Security Council has summoned an emergency meeting in response to the threat.
