At 7:29 am (2229 GMT Monday), the country's missile alert warning system was activated, with screens showing national broadcaster NHK turning to the alert message.

"North Korea appears to have launched a missile. Please evacuate into buildings or underground," the alert read.

NHK said the alert was in effect for two northern regions of the country, where the missile was believed to be headed.

Around 8:00 am, the prime minister's office then tweeted that "a projectile that appears to be a North Korean ballistic missile has likely flown over Japan".

In a statement, Japan's coastguard said the missile appeared to have already landed in the sea and warned vessels not to approach any falling objects.