The launch initially prompted the activation of a missile warning system for the southern region.

"Missile launch. Missile launch. North Korea appears to have launched a missile. Please take shelters inside buildings or underground," said the alert tweeted by the prime minister's office and carried on national broadcaster NHK.

But around 30 minutes later, the government tweeted that the alert was being cancelled.

"It is expected that the missile reported earlier will not come to Japan. The call for evacuation is lifted," it said.

Japan has activated its missile early warning alarms on several previous occasions in response to launches by Pyongyang, although the alerts are usually lifted quickly.