The launch, from near Pyongyang, came after the United Nations Security Council imposed an eighth set of sanctions on the country over its ballistic missile and atomic weapons programmes.
That was in response to its sixth nuclear test -- by far its largest yet -- earlier this month, which Pyongyang said was a hydrogen bomb small enough to fit onto a missile.
The North has raised tensions in the region with its rapid progress in weapons technology under leader Kim Jong-Un, who is closely associated with the programme and regularly pictured by state media overseeing launches and visiting facilities.
The missile flew over Hokkaido in northern Japan "at around 07:06 am (2206 GMT) towards the Pacific Ocean", Japan's J-Alert system said, with reports saying it came down around 2,000 kilometres east of Hokkaido.
"Japan can never tolerate this repeated provocative action by North Korea," Tokyo's top government spokesman told reporters.
"We have strongly protested to the North, telling them the strong anger by the Japanese people and condemn with the strongest words possible.'
It was fired from a similar location near the capital's airport, it added.
The South's President Moon Jae-In called an emergency meeting of Seoul's national security council, a standard procedure after the North fires a missile or tests a nuclear device.
Seoul's military carried out a ballistic missile drill of its own on Friday in the East Sea, Korea's name for the Sea of Japan, the Yonhap news agency reported.
In July, Pyongyang fired two intercontinental ballistic missiles that appeared to bring much of the US mainland into range.
US President Donald Trump threatened it with "fire and fury", heightening fears of conflict.
The United Nations Security Council sanctions imposed on Monday are the strongest so far, banning the North's textile trade and imposing restrictions on shipments of oil products, among a series of other measures.
But analysts expect them to do little to dissuade Pyongyang, which says it needs nuclear weapons to defend itself against the threat of invasion by the US.
Disclaimer: No Business Standard Journalist was involved in creation of this content
