Japanese PM Shinzo Abe called the move an “unprecedented” threat to his country.
The missile, launched early on August 29, flew over Hokkaido Island before crashing into the sea.
The UN Security Council is expected to hold an emergency meeting in response.
North Korea has conducted a flurry of missile tests recently, but this is the first time it has fired what is thought to be a ballistic weapon over Japan.
On the two previous occasions its rockets crossed Japan – in 1998 and 2009 – North Korea said they were for satellite launch vehicles, not weapons.
According to the South Korean military, the missile was fired eastward just before 06:00 local time from near Pyongyang – which is rare.
Early analysis of the launch suggests the missile flew a distance of more than 1,680 miles and reached a maximum altitude of about 342 miles, lower than most previous North Korean tests. The missile was likely a Hwasong-12, a newly developed intermediate range weapon, and fell into the North Pacific Ocean 740 miles off the Japanese coast after breaking into three pieces.
No effort was made by the Japanese to shoot down the missile but it issued a safety warning telling citizens in Hokkaido to take shelter in “a sturdy building or basement”.
US and Japanese forces are currently taking part in training drills in Hokkaido.
South Korea’s President Moon Jae-in ordered a show of “overwhelming” force in response to the launch. Four South Korean jets staged a live bombing drill on August 29.
Japan’s PM Shinzo Abe said he had spoken to President Donald Trump and that both agreed to increase pressure on North Korea.
Shinzo Abe said the North Korea’s “reckless action is an unprecedented, serious and a grave threat to our nation” which also “greatly damages regional peace and security”.
The prime minister said his government was doing its utmost to protect people’s lives.
North Korea’s conventional and nuclear weapons programs are a breach of international sanctions, so the test is being seen as a major provocation and an escalation of tensions on the Korean peninsula.
Earlier this month, North Korea threatened to fire missiles towards the US Pacific territory of Guam, while President Donald Trump warned Pyongyang would face “fire and fury” if it continued to threaten the US.
There have also been some reports in recent months that North Korea is preparing to carry out its sixth nuclear test.
However, last week, Secretary of State Rex Tillerson said the fact that North Korea had not carried out any missile launches since the UN imposed a fresh round of sanctions was an indication of restraint by Pyongyang.
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