North Korea fired an unidentified ballistic missile early on Friday from the capital Pyongyang that flew over northern Japan.
The projectile was launched at 6:57am (21:57GMT Thursday) and flew over the northern Japanese island of Hokkaido before falling into the Pacific Ocean - 2,000km east of Cape Erimo, said Japan's Chief Cabinet Secretary Yoshihide Suga.
"Japan protests the latest launch in the strongest terms and will take appropriate and timely action at the United Nations and elsewhere, staying in close contact with the United States and South Korea," Suga told reporters.
South Korea's defence ministry said the missile travelled about 3,700km and reached a maximum altitude of 770km - both higher and further than previous tests.
The ministry said the South's military conducted a live-fire ballistic missile drill in response to the North's launch.
The South Korean and US militaries are analysing details of the launch, the South's Office of the Joint Chiefs of Staff said. South Korea's presidential Blue House called an urgent National Security Council meeting.
The North's launch comes a day after Pyongyang threatened to sink Japan and reduce the United States to "ashes and darkness" for supporting a UN Security Council resolution imposing new sanctions against it for its September 3 nuclear test.
The North previously launched a ballistic missile from Sunan near the capital on August 29, which flew over Japan's Hokkaido island and landed in the Pacific waters.
Friday’s launch came after the United Nations Security Council imposed an eighth set of sanctions on the country over its banned missile and nuclear programmes.
The North has raised tensions in the region with its rapid progress in weapons technology under leader Kim Jong-un, who is closely associated with the programme and regularly pictured by state media overseeing launches and visiting facilities.