The test has been universally condemned by a host of countries who see it as a clear sign the regime is ratcheting up tensions with the international community.
Kim Jong-un’s latest missile carried a nuclear payload which was sent over Japan and splashed into the northern Pacific Ocean.
The aggressive missile launch on Tuesday – the longest ever from the North – over the territory of a close US ally sends a clear message of defiance as Washington and Seoul conduct war games nearby.
Kim’s test will anger US president Donald Trump as it looks especially aggressive to Washington, Seoul and Tokyo.
The action puts the North a step closer toward its goal of an arsenal of nuclear missiles that can reliably target the United States.
And it comes after a war of words between Pyongyang’s despot Kim and the US just subsided after the North threatened to launch missiles in Guam and Mr Trump vowed North Korea would be met with “fire and fury” if the hermit state dared to launch an attack.
Things had appeared calm in recent weeks, after Mr Trump hinted that he thought Kim now “respected” the US.
Mr Trump praised the North Korean leader for backing off on plans to fire missiles toward the US Pacific territory of Guam.
However, the North has shown it will not back down.
Senator Lindsey Graham a South Carolina Republican on the Armed Services Committee, condemned the test, and called it “a big-time escalation of conflict”.
The North has conducted launches at an unusually fast pace this year – 13 times, Seoul says – and some analysts believe Pyongyang could have viable long-range nuclear missiles before the end of President Trump’s first term in early 2021.
South Korea’s joint chiefs of staff said the missile traveled around 2,700 kilometres (1,677 miles) and reached a maximum height of 550 kilometres (341 miles) as it traveled over the northern Japanese island of Hokkaido.
The South Korean military was analysing whether the North had launched the Hwasong-12, a new intermediate-range missile that Pyongyang recently threatened to fire into waters near Guam, which hosts a major US military base the North considers a threat.
Jeffrey Lewis, director of the East Asia Nonproliferation Program at the Middlebury Institute of International Studies Monterey, said “early reports indicate that North Korea flew a Hwasong-12 [intermediate-range ballistic missile] over Japan”.
He added: “Why is anyone surprised? In June, North Korea warned ‘even if what we launch flies over Japan, Japan cannot say anything, even if it has hundreds of mouths.’”
Residents on Hokkaido were warned of a North Korean missile launch by a “J-Alert” on their cellphones, with loud alarms and an email that told people to stay indoors.
A radio speaker broadcast an alert saying “missile is passing, missile is passing”.
The test has worried the Japanese prime minister.
Shinzo Abe said: “We will do our utmost to protect people’s lives.
“This reckless act of launching a missile that flies over our country is an unprecedented, serious and important threat.”
The length and type of the missile test seemed designed to show North Korea can back up a threat to target the US territory of Guam, if it chooses to do so, while also establishing a potentially dangerous precedent of sending future missile tests over Japan.
Tokyo said there was no reported damage from the missile, which Japan’s NHK TV said separated into three parts.
Seoul says that while the North has twice before fired rockets it said were carrying satellites over Japan – in 1998 and 2009 – it has never before used a ballistic missile, which is unambiguously designed for military strikes.