No effort was made by the Japanese to shoot down the missile, which was launched early in the morning local time, triggering safety warnings.
The missile broke into three pieces before it landed, local media reported.
On Saturday North Korea fired three short-range missiles into the sea off its eastern coast.
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.
Japanese Prime Minister Shinzo Abe said shortly afterwards the government was doing its utmost to protect people's lives.
Chief Cabinet Secretary Yoshihide Suga described the latest test as "an unprecedented, grave threat". He said that Japan would take "appropriate steps" in response.
North Korea has fired a missile that flew over northern Japan before crashing into the sea, the Japanese government says.