The country's warning system for robot attacks was activated around 00.30 on Tuesday night Swedish time.
“North Korea appears to have launched a robot.
Please evacuate to buildings or underground," reads the warning message from the government.
The Japanese Prime Minister's Office writes on Twitter that "a projectile that appears to be a North Korean ballistic robot has likely flown over Japan".
Record number of weapons tests
From the South Korean side, it is confirmed that a robot was fired and its direction.
"North Korea fired an unidentified ballistic missile eastward," South Korea's defense ministry said in a statement.
The reclusive dictatorship has carried out a record number of weapons tests this year – four short-range missiles were fired last week alone.
Pyongyang's increasingly intensive weapons tests are taking place in parallel with Seoul, Tokyo and Washington increasing their joint military exercises