Washington quickly hit back, with the State Department saying it was aware of the reports and warning it was prepared to "defend ourselves and our allies from any attack or provocation".
The latest test also comes amid mounting tensions ahead of a planned US-South Korea joint military exercise later this month. Last year the drills involved 30,000 US soldiers and 50,000 South Korean troops.
The missile was launched from near the western North Korea city of Unyul at around 07:50 am today, South Korea's defence ministry said.
Japan's defence minister Gen Nakatani told reporters the missile was estimated to have fallen into Tokyo's exclusive economic zone 250 kilometres off its northern coast at 8:05 am today.
The test follows the launch of three ballistic missiles on July 19 in what the North said were simulated nuclear strikes on the South.
Pyongyang has carried out a series of missile tests this year in defiance of tough UN sanctions, and vowed to take "physical action" against the planned deployment of a US missile defence system in the South announced in July.
UN resolutions prohibit North Korea from developing ballistic missile technology.
Pyongyang has repeatedly warned of pre-emptive nuclear strikes against the South and US targets, although the main focus of its nuclear weapons programme is to develop a credible strike threat against the US mainland.
North Korea-US tensions had already been stoked by Pyongyang's fury at Washington's decision to personally target Kim with sanctions related to human rights abuses.
Together with the Key Resolve/Foal Eagle exercise, the Ulchi Freedom Guardian to be held this month is one of the two US-South Korea joint military exercises that are carried out every year on a massive scale.
