Early on Thursday, the country's J-Alert system was activated and residents in the northern Miyagi, Niigata and Yamagata regions were sent warnings to take shelter or stay indoors, with television stations breaking into regular programming to share the news.

The prime minister's office initially said a missile flew over Japan at around 7:48 am (2248 GMT Wednesday), but the country's defence minister subsequently said the alert had been issued in error.

"The missile was detected as having the potential to fly over the Japanese archipelago, so the J-Alert was issued," Defence Minister Yasukazu Hamada told reporters.

"After checking this information, we confirmed that the missile did not cross the Japanese archipelago, but disappeared over the Sea of Japan."

"We're analysing the reason" it disappeared, he added.

It came after another missile fired by North Korea travelled over Japan on October 4, and a day after Pyongyang launched a barrage of missiles and artillery towards South Korea.

National broadcaster NHK said Japan's government had not given an order to intercept the missile, which also prompted a brief suspension of the country's bullet train system in some areas.

"The continuous barrage of missiles day after day is an outrage and cannot be tolerated," Prime Minister Fumio Kishida told reporters.