North Korea fired a missile early on Tuesday that flew over northern Japan before crashing into the sea off the coast of Hokkaido, reports BBC.
The launch marks a sharp escalation of tensions with Japanese Prime Minister Shinzo Abe calling it an "unprecedented" threat.
North Korea has conducted a flurry of missile tests in recent month, but firing projectiles over Japan is rare.
Japan and the US have requested a UN Security Council meeting in response.
The South Korean military said that the missile was fired eastward from near the North's capital Pyongyang and flew a distance of more than 2,700km (1,678 miles).
It passed through the sky over Japan at a maximum altitude of about 550km (342 miles), the military said, and fell into the North Pacific Ocean 1,180km off the Japanese coast.
No effort was made by the Japanese to shoot down the missile but it triggered a safety warning in the region advising citizens in Hokkaido to take shelter in "a sturdy building or basement".
Mr Abe called the launch an "outrageous act" and an "unprecedented, serious and grave threat [that] greatly damages regional peace and security".
He said his government was doing its utmost to protect people's lives.
Given the missile's flight path the test is being seen as an escalation of tensions on the Korean peninsula.
On the two previous occasions North Korea fired rockets over Japan - once in 1998 and again in 2009 - the North claimed they were for satellite launches, not weapons.
Earlier this month, North Korea threatened to fire missiles towards the US Pacific territory of Guam, while US President Donald Trump warned Pyongyang would face "fire and fury" if it threatened the US.
There have also been some reports in recent months that North Korea is preparing to carry out its sixth nuclear test.