South Korea's and Japan's defence authorities said the missile flew around 700km and they both issued statements condemning the action.
South Korea's Office of National Security convened an emergency meeting, expressing concern over North Korea's continued ballistic missile launches following a previous launch on August 6. It urged Pyongyang to halt provocations that violate UN Security Council resolutions.
South Korea's military said it was maintaining readiness to respond "overwhelmingly" to any provocation under its combined defence posture with the United States.
There was no immediate statement from Pyongyang on the launch.
The missile, which landed in the sea outside Japan's exclusive economic zone (EEZ), reached a maximum altitude of about 90km, Japan's defence ministry said in a post on X.
"Japan lodged a strong protest with North Korea through diplomatic channels at the Japanese Embassy in Beijing and strongly condemned the action," Japan's Defence Minister Shinjiro Koizumi told reporters.
North Korea launched the missile from the Wonsan area on its east coast around 7am AEST on Wednesday, South Korea's Joint Chiefs of Staff said.
The launch came as South Korea and the United States plan to conduct major joint military drills from August 17-27, aimed at countering North Korea's evolving nuclear and weapons capabilities.
On Tuesday, North Korean state media condemned Japan's latest defence white paper as a document aimed at reviving militarism, saying Tokyo was using what it called an unfounded portrayal of Pyongyang as a security threat to justify an arms build-up.
North Korea has conducted a series of tests this year, including short-range ballistic missiles, artillery rockets and other tactical weapons.
Ukrainian President Volodymyr Zelenskiy said Moscow used a North Korean ballistic missile during a Russian attack on Tuesday that killed seven workers at a Ukrainian steel plant in the southeastern city of Zaporizhzhia.
