A North Korean missile passed over Japan early on Tuesday morning, local time. It broke into three pieces and fell into the waters 1,180 kilometers east (about 730 miles) of Japan's northern Hokkaido island, according to public broadcaster NHK.
Japan's top government spokesman said: "This ballistic missile launch appeared to fly over our territory. It is an unprecedented, serious and grave threat to our nation," Chief Cabinet Scretary Yoshihide Suga said. He called it a clear violation of United Nations resolutions.
Read more: Where did North Korea get its missile technology?
South Korea's military said the projectile was fired from the Sunan region near the North Korean capital of Pyongyang just before 6 a.m. (2100 UTC Monday). It did not try to shoot the missile down.
Japan's government had warned people in the north of the country to take precautions. The island nation's military is currently practicing deploying anti-missile batteries at three US bases in Japan.
South Korean officials had warned on Monday of signs that Pyongyang was preparing for another nuclear weapons test.
Weekend tests
On Saturday, North Korea test-fired three short-range ballistic missiles from Kittaeryong on North Korea's east coast. Two missiles flew about 155 miles (250 kilometers) in a northeastern direction and a third blew up almost immediately.
Read more: What is China's role in the North Korean crisis?
The Pentagon said the weekend launches did not threaten US territory - either the mainland or the US island territory of Guam - but Pentagon spokesman Colonel Robert Manning said, "You're still firing missiles, so that's a threat."
"We have to make the assumption that they continue to learn throughout each one of these missile launches," Manning said.
North Korea previously fired two intercontinental ballistic missiles in July.
South Korea and the US are holding annual defensive drills, which North Korea routinely describes as preparation for invasion.