The missile landed in the sea roughly 210km (130 miles) west of Hokkaido.
The US has condemned the launch, while South Korea has ordered stronger deterrence measures against the North.
North Korea has warned Japan that it will “pay a high price” if the alleged persecution of its nationals in the country continues.
According to South Korean news outlet Yonhap, the statement apparently referred to reports of an increase in hate crimes against students at schools across Japan for ethnic Koreans.
“We’ve solemnly stated that the October 4 firing of a new type of a ground-to-ground intermediate-range ballistic missile is a warning to our enemies,” adding that Tokyo will “pay a high price” for actions aimed against North Korea, KCNA said.
On Thursday North Korean FM Choe Son Hui warned of a “fiercer” response to any increased US military presence in the region.
It also launched a short range ballistic missile the same day.
That followed Sunday’s meeting between South Korean President Yoon Suk-yeol, US President Joe Biden and Japan’s PM Fumio Kishida in Cambodia, in which the three countries agreed to increase their military co-operation.
On Friday US National Security Council spokeswoman Adrienne Watson said Mr Biden had been briefed and the US would consult with partners.
North Korea has fired more than 50 missiles over the past two months, most of them short-range. These long-range launches are rarer, and pose a direct threat to the US, as the missiles are designed to carry nuclear warheads to anywhere on the US mainland.
The latest intercontinential ballistic missile (ICBM) was fired at 10:15 local time (02:15 GMT) from near the North Korean capital Pyongyang, military chiefs in Seoul said.
It reached an altitude of 6,100km on a lofted trajectory and travelled 1,000km (621 miles), reaching a speed of Mach 22, South Korea’s military said.
A lofted trajectory means the missile flies much higher into space but across a shorter distance than it would if fired on a normal trajectory.
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But Japan’s defence minister Yasukazu Hamada said the missile had sufficient range to reach the US.