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"I have received information that North Korea once again conducted a missile firing," he said. "We will immediately analyze information and do our utmost to protect the safety of the Japanese people."
There was no immediate announcement of the type of missile. On July 4, North Korea test-launched its first intercontinental ballistic missile.
Japanese government spokesman Yoshihide Suga said the missile launched today flew for about 45 minutes and landed off the Japanese coast in waters between Japan and the Korean Peninsula.
Japanese public broadcaster NHK said the coast guard issued safety warnings to aircraft and ships.
South Korea and the United States also confirmed the launch.
"We are assessing and will have more information soon," said Pentagon spokesman Navy Capt. Jeff Davis.
South Korea's Joint Chiefs of Staff said the missile was launched from North Korea's northern Jagang province.
Analysts say the "Hwasong 14" ICBM launched by North Korea on July 4 could be capable of reaching most of Alaska or possibly Hawaii if fired in an attacking trajectory.
It was launched at a very steep angle, a technique called lofting, and reached a height of more than 2,500 kilometers before splashing down in the Pacific Ocean 930 kilometers away.
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