Japanese Chief Cabinet Secretary Yoshihide Suga said the missile flew for about 45 minutes - longer than the ICBM tested in early July.
He said it landed in the sea in Japan's exclusive economic zone - not within Japan's territorial waters.
South Korea's President Moon Jae-in has convened an emergency security meeting for the middle of the night, Yonhap said.
Despite ongoing tests, experts believe Pyongyang does not yet have the capability to miniaturise a nuclear warhead, fit it onto a long-range missile, and ensure it is protected until delivery to the target.
They say many of North Korea's missiles cannot accurately hit targets.
But others believe that at the rate it is going, Pyongyang may overcome these challenges and develop a nuclear weapon within five to 10 years that could strike the US.
The US has installed a missile defence system in South Korea to combat the threat from the North, but the Terminal High-Altitude Area Defense system (Thaad) has angered many in the region, especially China.