The missile was launched "within the last 90 minutes," Colonel Rob Manning, a Pentagon spokesman, said around 2200 GMT Monday (6:30 am Tuesday in Pyongyang).
"We assess North Korea conducted a missile launch within the last 90 minutes. We can confirm that the missile launched by North Korea flew over Japan," Manning added, cautioning that the United States was still assessing the launch.
However, North American Aerospace Defense Command (NORAD) "determined the missile launch from North Korea did not pose a threat to North America," Manning said.
South Korea's Joint Chiefs of Staff said in a statement that the missile was launched around 2057 GMT Monday from Sunan, near Pyongyang, and traveled east "and over Japan."
It travelled around 1,700 miles (2,700 kilometers) at a maximum altitude of around 350 miles, it said, adding that South Korea and the US were "closely analysing for more details."
North Korea's missile launch over Japan has been denounced as highly provocative by federal Labor.
Opposition foreign affairs spokeswoman Penny Wong told ABC radio if the reports were correct: "(it) is a highly provocative unlawful action by North Korea".
Japan precautions
The government's J-Alert warning system advised people in the area to take precautions, but public broadcaster NHK said there was no sign of damage.
The Japanese military did not attempt to shoot down the missile, which passed over Japanese territory around 6:06 a.m. local time (2106 GMT).
The missile broke into three pieces and fell into waters 1180km east of Hokkaido, NHK said.
Japan's Chief Cabinet Secretary Yoshihide Suga said on Tuesday that North Korea's latest missile launch was a threat that Tokyo would respond to firmly.
"This ballistic missile launch appeared to fly over our territory. It is an unprecedented, serious and grave threat to our nation," the top government spokesman told reporters.
