Japanese authorities later retracted the alert, saying an emergency warning system had made an erroneous prediction the missile would fall near the island.
Japan's coast guard said the projectile that appeared to be the missile had fallen in the sea to the east of North Korea.
The launch came days after North Korean leader Kim Jong Un called for a strengthening of the country's war deterrence in a "more practical and offensive" manner to counter what the country called moves of aggression by the United States.
The missile, suspected to be intermediate-range or longer, was fired at 7.23am from near Pyongyang, South Korea's Joint Chiefs of Staff (JCS) said.
The South Korean military said it was on high alert and maintaining a readiness posture in close coordination with the US.
The missile fell outside Japan's exclusive economic zone, Japan's Kyodo news agency reported.
North Korea has criticised a recent series of joint military exercises between the US and South Korea as escalating tensions, stepping up its weapons tests in recent months.
- Reuters