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South Korean military officials reportedly said that the missile was fired from an airfield near Pyongyang, North Korea's capital, and headed eastward.
Japan did not attempt to shoot down the missile, NHK reported.
In response to the latest provocation, South Korea is reportedly conducting a ballistic missile drill in the East Sea.
A North Korean state agency threatened on Thursday to use nuclear weapons to "sink" Japan and reduce the United States to "ashes and darkness" for supporting a UN Security Council resolution and sanctions over its latest nuclear test, Reuters reported.
Experts estimate that this would be the sixth time a North Korean projectile has flown over Japan.
Japanese official says the country's govt will take appropriate response to North Korea firing missile and it is in contact with U.S. - SKY
In response, South Korea held a ballistic missile drill of its own.
The United States is aware and are monitoring the incident.