The launch is the second to fly over Japan in less than a month, and the first since North Korea’s sixth nuclear test and new UN sanctions against the Kim Jong-un regime, reports CNN.
The missile was fired from Sunan district near Pyongyang, according to the South Korean military.
It flew about 3,700 km and reached an altitude of 770 km miles before landing in the Pacific Ocean.
Speaking to the media, Japanese Prime Minister Shinzo Abe said: “The international community needs to unite and send clear message after North Korea’s dangerous provocation.
“We must let North Korea understand there is no bright future for North Korea if it continues in this way.”
The Japanese government issued a J-Alert and advised “people to stay away from anything that could be missile debris”.
Pyongyang on Wednesday threatened the “four islands of the (Japanese) archipelago should be sunken into the sea by the nuclear bomb of Juche”, referring to the ruling ideology of North Korea.
In response to North Korea’s launch, South Korea carried out a “live fire drill” that included a missile test-firing which the Joint Chiefs of Staff said was capable of striking Pyongyang’s Sunan launch site.
Seoul’s missile, which was launched from the country’s east coast while the North Korean missile was still in the air, was “a show of force in response to North Korea’s latest provocation”, a South Korean official told CNN.
A second missile that was fired at the same time failed and “sank into the sea off the east coast”, the official said.
Japan and the US have requested the UN Security Council hold “urgent consultations” at 3 p.m. on Friday.
North Korea has fired 21 missiles during 14 tests since February this year, further perfecting its technology with each launch.