South Korea's military said Kim's regime fired the "unidentified projectile" from Pyongyang towards the sea at 5:57am local time.
The government's J-Alert warning system advised people in the area to take precautions.
But public broadcaster NHK said there was no sign of damage and the Japanese military did not attempt to shoot down the missile.
It passed over Japanese territory around 6:06 am local time, officials said.
Kim has sparked fury throughout the world this year by ramping up his missile programme and continuing to threaten the United States.
Donald Trump brought tensions with the North Korea to a new height as he outright threatened "fire and fury" against Pyongyan
