The launch is a direct challenge to the new South Korean president elected four days ago and comes as US, Japanese and European navies gather for joint war games in the Pacific.
It was not clear what type of ballistic missile was launched, although the US Pacific Command said that “the flight is not consistent with an intercontinental ballistic missile”.
Outside militaries will closely analyse what the North fired. While Pyongyang regularly tests shorter-range missiles, it is also working to master the technology needed to field nuclear-tipped missiles that can reach the US mainland.
Past North Korean missiles have flown farther than Sunday’s test, landing closer to Japan, but this launch follows a series of high-profile failures.
Whatever the type of missile, the launch forces the new South Korean leader, Moon Jae-in, to put dealing with Pyongyang above the domestic economic agenda he made a priority during his early days in office.
Mr Moon, a liberal who favours a softer approach to the North than his conservative predecessors, strongly condemned the launch during an emergency national security meeting.
He called it a clear violation of UN Security Council resolutions and a serious challenge to international peace and security, according to senior presidential secretary Yoon Young-chan.
“The president expressed deep regret over the fact that this provocation occurred just days after a new government was launched in South Korea,” Mr Yoon told a televised conference.
“The president said we are leaving open the possibility of dialogue with North Korea, but we should sternly deal with a provocation to prevent North Korea from miscalculating.”
Japanese Chief Cabinet Secretary Yoshihide Suga said the missile flew about 500 miles from a launch site on North Korea’s western coast for about 30 minutes and landed in the Sea of Japan, but not inside Japan’s exclusive economic zone.
Japan’s defence ministry said the missile probably reached an altitude of 1,240 miles.
Prime Minister Shinzo Abe told reporters on Sunday that the launch is “absolutely unacceptable” and that Japan will respond resolutely.
South Korea’s Joint Chiefs of Staff said the missile was fired early on Sunday morning from near Kusong, in North Phyongan province.
North Korea’s past satellite rocket launches have been called clandestine tests of ICBM technology, but it is not believed to have tested a true intercontinental ballistic missile yet.
The White House said President Donald Trump “cannot imagine that Russia is pleased” with North Korea’s latest missile test because the missile landed so close to Russian soil.
It said the US maintains its “ironclad commitment” to stand with its allies in the face of the serious threat posed by North Korea.
The latest “provocation” should serve as a call for all nations to implement far stronger sanctions against the North, the White House said.
The North’s state media had said on Saturday the nation will bolster its nuclear capability unless the US abandons its hostile policy.
“The United States should never expect us to give up our nuclear capability,” the main Rodong newspaper said in a commentary carried by the Korean Central News Agency.
It said Mr Trump’s “maximum pressure and engagement” policy is only aimed at “stifling us” and will compel the North to “strengthen our nuclear deterrent at the maximum speed”.
The launch also comes as troops from the US, Japan and two European nations gather on remote US islands in the Pacific for drills that are partly a message to North Korea.
The USS Carl Vinson, an aircraft supercarrier, is also engaging with South Korean navy ships in waters off the Korean Peninsula.
Last week South Koreans elected Mr Moon to replace conservative Park Geun-hye, who is in jail awaiting a corruption trial.
He is the first liberal leader in Seoul in nearly a decade, and said as he took his oath of office that he would be willing to visit the North if the circumstances were right.