According to both countries, the launch that took place early Tuesday marked Pyongyang's first missile to fly over Japan in five years.
South Korea's Joint Chiefs of Staff said it appeared to have been an intermediate-range ballistic missile (IRBM) launched from North Korea's Jagang Province. North Korea has used that province to launch several recent tests, including multiple missiles that it claimed were hypersonic.
Tokyo urged residents to shelter themselves and suspended train operations in the area, which was overflown by the North's projectile.
The missile fell into the Pacific Ocean after flying "over and past" Japan's territory, the Japanese government said.
South Korea's Joint Chiefs of Staff, meanwhile, said the South's military was "maintaining a full readiness posture and closely cooperating with the United States while strengthening surveillance and vigilance."
"North Korea's series of actions, including its repeated ballistic missile launches, threaten the peace and security of Japan ... and pose a serious challenge to the entire international community, including Japan," Japan's top government spokesperson Hirokazu Matsuno, told a news conference.
The test prompted East Japan Railway Co to suspend train operations in the northern regions, Japanese broadcaster NHK reported. Matsuno said there were no reports of damage to aircraft or ships from the missile.
He said the North's missile flew 4,600 kilometers (2,850 miles) to a maximum altitude of 1,000 km.
The new missile launch came less than a week after South Korea, Japan, and the US staged anti-submarine drills.
Last week, Pyongyang fired short-range ballistic missiles on four occasions, including just hours after US Vice President Kamala Harris flew out of Seoul.
ZZ/PR