The prime minister's office said a missile flew over Japan at around 7:48 am, but national broadcaster NHK said subsequently that officials were analysing the possibility that the missile did not, in fact, travel over the country.

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.

Television broadcasters broke into programming to urge residents in the Miyagi, Niigata and Yamagata regions to take shelter or stay indoors.

"Please alert police and fire departments when finding suspicious objects and do not go near them," the prime minister's office said in a tweet.

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 government's top spokesman is expected to speak to reporters shortly.