Japan's upgraded missile response system swung into action, sending emergency alerts through cellphones and over loud speakers, warning people on the potential flight path of the threat and advising them to take cover.
This missile appears to have been a Hwasong-12, an intermediate range ballistic missile technically capable of flying 4830km, easily putting the US territory of Guam within reach. However, the missile flew east, over Hokkaido and into the Pacific Ocean, rather than on a southward path toward Guam.
Still, the latest launches, coming after North Korea last month launched two intercontinental ballistic missiles theoretically capable of reaching the mainland United States, underscore both Kim's defiance of the international community and his determination to press ahead with his missile programme.
The White House did not immediately respond to the latest provocation, but analysts said it marked a worrying escalation.
"This is a much more dangerous style of test," said Abraham Denmark, director of the Asia programme at the Kissinger Institute and a former top East Asia official at the Pentagon.
North Korea's recent missile tests had been carefully calibrated to go nearly straight up and land in the sea between the Korean Peninsula and Japan, rather than overflying Japan.
"North Korean missiles have a habit of breaking apart in flight so if this happened and parts of it landed in Japan, even if it was not North Korea's intention, this would amount to a de facto attack on Japan," Denmark said.
This missile appeared to have broken into three during flight, but all of the parts landed in the sea.
The missile was launched from a site at Sunan, north of Pyongyang. Sunan is the location of the country's main international airport and the arrival point for outside visitors to the country.
US intelligence agencies were monitoring the site and had seen signs of the impending launch hours earlier, when they spotted Hwasong-12 missile equipment being moved into place.
The Hwasong-12, known to American agencies as the KN-17, is fired from a road-mobile launcher - usually a modified truck - making it easy to move around the country and launch at short notice.
North Korea has sent a missile over Japan before, in 1998. Part of a North Korean rocket also flew over Japan in 2009, although Pyongyang claimed it was a satellite launch and it gave Japan notice before the launch.
This time, there was no notice.
The missile travelled 1180km to land in the Pacific Ocean east of Hokkaido's Cape Erimo.
The Japanese broadcaster NHK showed Patriot missiles lined up in Japan, a staunch US ally, ready to shoot down any incoming missiles. However, Japan did not use any of its missile defences, apparently because the projectiles were not heading to Japanese territory.
"We will make every possible effort to protect citizens' lives and property," Abe told reporters before heading into the national security council meeting.
South Korea's joint chiefs of staff also confirmed that the missile had passed over Japan.
The launch, on the heels of three short-range missiles fired at the weekend, come amid ongoing joint exercises between the United States and South Korean militaries, exercises that North Korea always strongly protests because it considers them preparation for an invasion.
The exercises, which mainly involve computer simulations rather than battlefield maneuvers, are due to end on Thursday.
"We should expect a kinetic reaction from North Korea during the exercises, but this pushes the boundaries of an ordinary response," said Daryl Kimball, the director of the Arms Control Association.
However, Kimball said that talks still remained the best course of action for dealing with North Korea.
"The US and Japan have so few options to respond to these ballistic missile tests short of negotiations that would have North Korea agree to halt these launches in return for a modification of future military exercises," he said. "This is why North Korea is such a problem - there are no good options."
The launches mark a dangerous new escalation from Kim's regime.
Kim - who has ordered the launch of 18 missiles this year alone, compared to the 16 missiles his father, Kim Jong Il, fired during 17 years in power - has defied international calls to stop his provocations.
Missile launches and nuclear tests are banned by the United Nations Security Council. But Kim has pressed ahead unrelentingly.
His Government had been threatening to fire a missile to pass over Japan and land near Guam, the American territory in the Pacific Ocean that is home to two huge US military bases, by the middle of this month. North Korea listed prefectures including Hiroshima, Ehime and Kochi as on the flight path. However, Kim later said that after reviewing the plans, he would "watch the Yankees a little longer" before making a decision whether to launch.
After the Guam threat, Trump warned North Korea that "things will happen to them like they never thought possible" should the isolated country attack the United States or its allies.
With no missile launches during the first three weeks of August, the Trump Administration had suggested its tough talk was working, with Trump saying last week at a rally in Phoenix that Kim had come to "respect" him. This echoed an earlier assessment by Secretary of State Rex Tillerson.
