The US military said the North had actually launched two Rodong intermediate-range missiles simultaneously, but one appeared to have exploded on take-off.
The launches followed a North Korean threat of "physical action" over the planned deployment of a sophisticated US anti-missile system in South Korea, and came just weeks before the start of large-scale, joint South Korea-US military exercises.
Japan said the one missile had landed in the Sea of Japan, some 250 kilometres (155 miles) off its northern coast and within the country's Exclusive Economic Zone (EEZ).
The United States condemned what it called a clear violation of UN Security Council resolutions explicitly prohibiting North Korea's use of ballistic missile technology.
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"This provocation only serves to increase the international community's resolve to counter (North Korea's) prohibited activities," said Pentagon spokesman Gary Ross.
US Strategic Command said the two missiles were launched from a site in western North Korea at around 7:50am Seoul time.
"Initial indications reveal one of the missiles exploded immediately after launch, while the second was tracked over North Korea and into the Sea of Japan," it said in a statement.
Japan's top government spokesman Yoshihide Suga slammed Pyongyang for providing no advance warning of today's test.
"From the perspective of the safety of aircraft and ships, it is an extremely problematic, dangerous act," Suga said.
The Rodong is a scaled-up Scud variant with a maximum range of around 1,300 kilometres (800 miles).
Pyongyang has conducted a series of missile tests this year in defiance of UN sanctions imposed after its fourth nuclear test in January.