Millions of Japanese awoke to ominous text messages on Tuesday warning them to take cover as a North Korean missile flew overhead.

Sirens blared out in northern communities that were on the flight path of the ballistic missile as it soared over Japanese territory for two minutes before crashing into the Pacific.

“Missile passing. Missile passing,” warned an official text message sent to people across the north of Japan.

“A short time ago, a missile apparently passed above this area.If you find suspicious objects, please don't go near them and immediately call police or firefighters. Please take cover in secure buildings or underground,” it said.

North Korea's launch towards neighbouring Japan — a key US ally and Korea's former colonial overlord — marked a major escalation by Pyongyang amid tensions over its weapons ambitions. And for the first time in the most recent round of weaponised brinkmanship from Pyongyang, it brought real worries to people in Japan.

Morning commuters in northernmost Hokkaido were greeted by warning signs at train stations — bringing many rail services to a halt.

At one metro station in Sapporo, a major city of nearly two million, passengers were warned here would be delays. “All lines are experiencing disruption,” said one sign.

“Reason: Ballistic missile launch,” it added.

“Some passengers came down to take cover in a couple of subway stations,” a Sapporo subway spokesman told AFP.

Others had little choice but to carry on with their usual schedule, including the crews aboard some 15 fishing vessels that had already left port off southern Hokkaido in an area under the missile's path.

“I was surprised that it went above our area. This has never happened before,” Hiroyuki Iwafune, an official at the local fishery co-op, told AFP.

“I was worried. Everyone felt the same. But what can you do? Hide? But where? We called those who were at sea. But then they said, even with this (warning), what are we supposed to do?'” Iwafune added.

'Very dangerous'

In Tokyo, more than 700 kilometres south of the missile's flight path, some train services were temporarily halted. “Currently, a North Korean missile is flying above Japan,” said announcements at Tokyo stations handling bullet trains, minutes after the launch.

“It is very dangerous. Please take cover at the waiting areas or inside the trains,” it added.

Tokyo university student Julia Kotak said she was scared of the possibility that a missile could hit Japan. “But I don't think there is anything that we could do,” the 18-year-old told AFP.

At a US military base in Tokyo, Japan deployed a Patriot Advanced Capability-3 (PAC-3) missile defence system as part of a previously scheduled drill.

“Practising this kind of drill allows us to maintain our fast response system in the event of a ballistic missile launch and to strengthen the force of persuasion, not only by our country but also by the US-Japan alliance,” Hiroaki Maehara, commander of Japan's Air Self-Defence Forces, told a press briefing.