The missile blasted off from near the Sunan International Airport north of Pyongyang, the North Korean capital, and flew about 2,300 miles, flying over northern Japan, The New York Times quoted South Korean military as saying.
South Korea's presidential Blue House has called an urgent meeting of its national security council.
The Guardian quoted Japan's public broadcaster NHK as saying that the missile passed over the northern island of Hokkaido and landed in the Pacific about 2,000 km east of Japan. The government said there was no danger to people or shipping from missile debris.
The launch comes a day after Pyongyang threatened to sink Japan and reduce the United States to "ashes and darkness" for supporting a UN Security Council resolution (UNSC) imposing new sanctions against it for its 3 September nuclear test.
According to experts, North Korea on September 3 detonated its largest nuclear bomb to date, a device four to 16 times larger than anything it had previously tested
The sanctions are designed to accomplish six major goals: cap North Korea's oil imports, ban textile exports, end additional overseas labourer contracts, suppress smuggling efforts, stop joint ventures with other nations and sanction designated North Korean government entities.
North Korea has launched more than 80 missiles since Kim Jong-un came to power in 2011. (ANI)