No effort was made by the Japanese to shoot down the missile, which flew over Japanese territory at dawn.
The missile is reported to have broken into three pieces before it landed, local media reported.
On Saturday North Korea fired three short-range missiles into the sea.
In the latest incident the Japanese government warned people in the missile's flight range to take precautions, but public broadcaster NHK said there was no signs of any damage.
File Photo: Copyright KOREA NEWS SERVICE