The missile, which was launched from a port city known for its submarines, flew for nine minutes before splashing into the sea about 40 miles away, USA and South Korean officials said.
U.S. officials said the missile launched on Wednesday appeared to be a liquid-fuelled, extended-range Scud missile that only travelled a fraction of its range before spinning out of control.
"The test-firing was successful", the official was quoted as saying.
Though the White House has previously made similar statements, the call came hours before Trump hosts Chinese President Xi Jinping for a two-day summit at his Mar-a-Lago estate in Florida.
There has been no substantial progress in bilateral talks on the abduction issue, though North Korea agreed with Prime Minister Shinzo Abe's government in 2014 to reinvestigate the abductions of Japanese nationals.
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In response to another ballistic missile firing by North Korea - the third since President Trump took office - Secretary of State Rex Tillerson on Tuesday night gave what may be the bluntest USA response yet to the provocative action.
"The United States has spoken enough about North Korea". We have no further comment.
In addition to tougher sanctions and pressuring Beijing to rein in Pyongyang, Trump has also suggested that he will strengthen allied missile defense capabilities.
South Korea's defence ministry said: "The military is keeping a close watch over North Korea's provocative moves and maintaining a high defence posture". The Whitehouse also said on Tuesday that Trump would be sending a clear signal to Xi on North Korea, though would not discuss the specifics of his strategy.
Although the disappointment was evident on the faces of the North Korean players, they were gracious in defeat, leaving a memorable impression on the audience and the South Korean players. Sinpo is home to a North submarine base.
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North Korea's liquid fuel-powered ballistic missiles typically require a garrison, fuel storage tanks and support vehicles to launch, which can be identified with imagery, experts say. "But China has its own North Korean policy, independent of what the US might want". But the JCS said the missile was sacked ashore.
In a statement, the United Nations body described the conducting of missile tests by Pyongyang as "highly destabilizing behavior". It is likely to be an upgraded version of the submarine-launched missile named "Pukguksong" launched last summer.
Secretary of State Rex Tillerson's reaction to North Korea's latest missile launch tonight was short and sweet: he's over talking about it.
The command says it tracked the missile until it landed at 6:51 a.m.in the Sea of Japan.
Some analysts suggested that the launch might be another attempt to develop a new ballistic missile, saying it was unusual for the North to fire a missile at a launch site near the coast, not an inland site at Banghyeon, North Pyongan Province, where the North test-fired Pukguksong 2 in February and intermediate-range Musudan missiles past year.
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The test comes as South Korea, Japan and the USA wrap up trilateral naval military drills off the Korean Peninsula. The North will celebrate the birthday of its late founder and the current leader's grandfather, Kim Il Sung, on April 15 as well as the anniversary of the army's creation on April 25.