The missile flew over Japan, landing in the Pacific about 2,000 km (1,240 miles) east of Hokkaido, Japan Chief Cabinet Secretary Yoshihide Suga told reporters in a hastily organised media conference.
"These repeated provocations on the part of North Korea are unpermissible and we protest in the strongest words," Suga said.
The unidentified missile reached an altitude of about 770 km (480 miles) and flew 3,700 km (2,300 miles), according to South Korea's military - far enough to reach the U.S. Pacific territory of Guam.
Last month, North Korea fired a missile from similar area near the capital Pyongyang that also flew over Hokkaido into the ocean.
South Korea said it had fired a missile test into the sea to coincide with North Korea's launch. The presidential Blue House has called an urgent National Security Council meeting. Japan also convened a National Security Council meeting.
The North's launch comes a day after the North threatened to sink Japan and reduce the United States to "ashes and darkness" for supporting a U.N. Security Council resolution imposing new sanctions against it for its Sept. 3 nuclear test, its most powerful by far.
The North accuses the United States, which has 28,500 troops in South Korea, of planning to invade and regularly threatens to destroy it and its Asian allies.
Australia, a strong and vocal ally of the United States, quickly condemned the launch.
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