|North Korea has held a series of recent missile tests|
The Japanese government's warning system urged people in an area in the north of the country to take precautions early on Tuesday morning.
South Korea's military said the missile travelled 1,678 miles and was fired from North Korea's Sunan region, near the capital Pyongyang, just before 6am local time.
But Japan's military did not attempt to shoot down the missile, which broke into three pieces and fell into the sea east of Hokkaido.
There was no damage reported and the Pentagon said the missile posed no threat to US territory.
Foreign Secretary Boris Johnson condemned the latest missile launch, tweeting: "Outraged at reckless provocation by #NorthKorea. Strongly condemn latest illegal missile launch by #DPRK."
Earlier in August, North Korean leader Kim Jong Un had threatened to fire missiles at the US Pacific territory of Guam .
US President Donald Trump had promised "fire and fury" for North Korea if it threatened the US.
Tensions appeared to have eased in recent weeks, although North Korea has previously reacted angrily to US/South Korean military drills, such as the ones currently underway, which it describes as an invasion rehearsal.
|Hokkaido is in Japan's north, near where the missile fell apart|
Hokkaido is in Japan's north, near where the missile fell apart
"We will do our utmost to protect people's lives," he added.
"This reckless act of launching a missile that flies over our country is an unprecedented, serious and important threat."
US Secretary of State Rex Tillerson and South Korea's foreign minister agreed to consider tougher sanctions against North Korea following the missile launch.
Foreign affairs expert Tim Marshall told Sky News that the move by the North Koreans was "massively provocative" but added that we "may not be at the brink".
He said: "Crucially, the missile fell hundreds of miles outside Hokkaido and hundreds of miles from Guam.
"What this means is that the Americans can say it's not a threat, the Japanese patriot missile system...did not need to be fired and the North Korean leadership knew this, so they've made this massive gamble.
"It's the first time in years that they've fired a missile over Japan, everyone's gone into emergency mode, quite understandable, but at the moment the signals are this is still not going over the brink.
"But it's pretty close to it and when you get close to the brink, things can happen that you haven't planned for."
Mr Marshall added: "If this had been close to Guam, I think it could have triggered a war; if it had been so close to Hokkaido that the patriot missile system had to shoot it down then that might have triggered a war.
"That's why it is a calculated gamble from the North Koreans...it allowed some wiggle room."