The test, which experts said appeared to have been an intermediate-range Hwasong 12 missile, came as US and South Korean forces conduct annual military drills on the peninsula, against which North Korea strenuously objects.
North Korea has conducted dozens of ballistic missile tests under young leader Kim Jong-Un, the most recent on Saturday, but firing projectiles over mainland Japan is rare.
Japanese public broadcaster NHK reported the missile broke into three pieces and fell into waters off Hokkaido.
“North Korea’s reckless action is an unprecedented, serious and grave threat to our nation,” Japanese Prime Minister Shinzo Abe told reporters.
Abe and US President Donald Trump agreed in telephone talks to increase pressure on North Korea after the country’s latest missile launch.
Trump also said that the United States was “100 per cent with Japan” and he showed a strong commitment to Tokyo’s defence.
The test was a clear violation of UN resolutions and the government had protested against the move in the strongest terms, he said.
Australian Prime Minister Malcolm Turnbull condemned North Korea after receiving a security briefing on the missile launch.
“We condemn this latest missile test in the strongest terms,” he told FIVEaa radio today.
“The North Korean regime continues recklessly to threaten the peace and stability of the region and indeed of the world.”
Turnbull again called on all nations to impose the harshest sanctions on Pyongyang, singling out China as the country with the most economic leverage.
“They have the ability to bring North Korea to its senses without military action,” he said.
Japan’s Chief Cabinet Secretary Yoshihide Suga said the latest North Korean missile fell into the sea 1180km east of the Cape of Erimo on Hokkaido.
The Japanese government’s J-Alert system broke into radio and TV programming, warning citizens of the possible missile.
Bullet train services were temporarily halted and warnings went out over loudspeakers in towns in Hokkaido.
South Korea’s military said the missile was launched from the Sunan region near the North Korean capital just before 6am (7am AEST). It flew 2700 km, reaching an altitude of about 550km.
“We will respond strongly based on our steadfast alliance with the United States if North Korea continues nuclear and missile provocations,” the South’s foreign ministry said in a statement.
“It’s pretty unusual,” said Jeffrey Lewis, head of the East Asia Nonproliferation Program at the Middlebury Institute of Strategic Studies at Monterey, California.
“North Korea’s early space launches in 1998 and 2009 went over Japan, but that’s not the same thing as firing a missile.”
Masao Okonogi, professor emeritus at Japan’s Keio University, said: “(North Korea) think that by exhibiting their capability, the path to dialogue will open.”
“That logic, however, is not understood by the rest of the world, so it’s not easy,” he said.
In Washington, the Pentagon confirmed the missile flew over Japan but did not pose a threat to North America and said it was gathering further information.
North Korea has again asked the UN Security Council to meet to discuss the ongoing joint US-South Korean military drills, according to a letter released on Monday by the North Korean mission to the United Nations.
The August 25 letter to the Security Council and Secretary-General Antonio Guterres, from North Korean UN Ambassador Ja Song Nam, described the military exercises as a “grave threat” to the Korean peninsula and international peace and security.
“It is the fair and square self-defensive right of the DPRK to cope with reckless, aggressive war manoeuvres and the US would be wholly responsible for any catastrophic consequences to be entailed from the result,” Ja wrote, using the initials of North Korea’s official name, the Democratic People’s Republic of Korea.
Previous requests have gone unanswered by the 15-member Security Council.
The 15-member UN Security Council unanimously imposed new sanctions on North Korea in response to the two July long-range missile launches.
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