The Scud flew about 450km (280 miles) before landing in Japanese waters, prompting Japan to lodge a protest.
Observers say the tests indicate the North is making progress towards missiles capable of carrying warheads.
The North has repeatedly defied a UN resolution banning all nuclear and missile activity, and has ramped up its tests in recent months.
The US Pacific Command said the missile was launched from Wonsan in North Korea and flew for about six minutes before landing.
Japan’s chief cabinet secretary Yoshihide Suga told reporters that the missile landed in an area between Japan’s Sado and Oki islands, in their exclusive economic zone.
A spokesman for South Korea’s military said the missile reached an altitude of 120km, and “an analysis is under way on the specific number” of missiles fired, indicating that more than one could have been launched.
The launch comes a day after North Korea’s state media reported the test of a new anti-aircraft weapon system, and released pictures of leader Kim Jong-un watching the test.
North Korea has a large stockpile of short-range Scud missiles developed by the Soviet Union. Modified versions of the Scud missiles can have a range of 1,000km.