Emergency alerts warned Japanese residents of the launch and the Coastguard told ships to watch for falling debris.
But it was not immediately clear whether North Korea had launched another intercontinental ballistic missile capable of reaching the US mainland, or whether this was a shorter-range projectile.
"We are in the process of assessing the situation and will provide additional information when available," said Lieutenant Colonel Chris Logan, a Pentagon spokesman.
White House press secretary Sarah Huckabee Sanders tweeted that President Donald Trump "was briefed, while missile was still in the air, on the situation in North Korea".
There had been signs that North Korea was preparing for another launch. The Japanese government had detected radio signals suggesting that North Korea might be preparing for a ballistic missile launch, Kyodo News reported Monday, citing government sources.
North Korea last fired a missile on September 15, sending an intermediate-range missile over the northern Japanese island of Hokkaido. It travelled east for 3700km, landing in the Pacific Ocean.
North Korea was seeking military "equilibrium" with the United States as a way to stop American leaders from talking about military options for dealing with Pyongyang, North Korean leader Kim Jong Un said after supervising the September 15 launch.
That was the second launch over Japan in less than three weeks and came less than two weeks after North Korea exploded what was widely believed to be a hydrogen bomb.
Those events triggered ire overseas, with Trump denouncing North Korea's regime during a speech to the United Nations General Assembly and mocking Kim as "little rocket man".
That label triggered an angry and unusually direct response from the North Korean leader, who called Trump a "mentally deranged US dotard" and warned the US president that he would "pay dearly" for his threat to destroy North Korea.
On Tuesday, a senior South Korean official said North Korea could announce next year that it has completed its nuclear weapons programme.
"North Korea has been developing its nuclear weapons at a faster-than-expected pace. We cannot rule out the possibility that North Korea could announce its completion of a clear force within one year," Cho Myoung-gyon, the unification minister, who is in charge of the South's relations with the North, told foreign reporters in Seoul.
Pyongyang has been working to fit a nuclear warhead to a missile capable of reaching the US mainland, which it says it needs to protect itself from a "hostile" Washington. It has made rapid progress during the course of this year, firing two intercontinental ballistic missiles in July, the second of which was technically capable of reaching Denver or Chicago, or possibly even New York.
But despite an increase in tensions over the past two months, including a US Navy three-carrier strike group conducting military exercises in the sea between Japan and the Korean Peninsula, 74 days had passed without any missile launches by the North.
That was the longest pause all year, according to Shea Cotton, a research associate at the James Martin Centre for Nonproliferation Studies in Monterey, California. North Korea has now tested 20 missiles this year, compared with 24 by this time last year.
The pause had raised hopes that North Korea might be showing interest in returning to talks about its nuclear programme.
In a speech to the Council on Foreign Relations late last month, Joseph Yun, the State Department's special representative for North Korea policy, said that if North Korea went 60 days without testing a missile or a nuclear weapon, it could be a sign that Pyongyang was open to dialogue.
