World War 3 fears were sparked when North Korea fired a missile more than 2,300 miles – a distance experts claim puts the US territory of Guam within range of another strike.
Alerts blared out across northern Japan as the missile passed at a height of around 500 miles before crashing into the sea.
US Secretary of Defence Jim Mattis said the launch “put millions of Japanese into duck and cover”, although reports suggest the majority of residents in northern Japan appeared calm and went about their business as normal.
Warning announcements about the missile blared around 7am (2200 GMT Thursday) in the town of Kamaishi in northern Japan, footage from national broadcaster NHK showed.
Citizens were warned that debris could still fall on the island nation.
Last month, North Korea fired an intermediate range missile from a similar area near the capital Pyongyang that also flew over Hokkaido into the ocean and said more would follow.
Hokkaido resident Andrew Kaz said: “The first time was unexpected, but I think people are getting used to this as the new normal.
“The most it seemed to disrupt was my coffee.”