The US defence department said Friday's launch appeared to be that of a long-range ICBM.
After South Korea's military and Shinzo Abe, Japan's prime minister, confirmed the report, the governments in Seoul and Tokyo convened meetings of their national security councils.
US President Donald Trump said the missile launch was "only the latest reckless and dangerous action by the North Korean regime".
He said the US "will take all necessary steps to ensure the security of the American homeland and protect our allies in the region".
Captain Jeff Davis, a Pentagon spokesperson, said the launch took place at about 14:45 GMT from Mupyong-ni, an arms plant in northern North Korea.
South Korea's Yonhap news agency, citing the country's military joint chiefs of staff, said the missile was launched from Jagang province, and landed in the East Sea.
The launch left analysts concluding that a wide swath of the US is now in range of North Korean weapons.
David Wright, a physicist and co-director of the global security programme at the Union of Concerned Scientists, told the Associated Press news agency that if reports of the missile's maximum altitude and flight time are correct, it would have a theoretical range of at least 10,400 kilometres.
That means it could have reached Los Angeles, Denver or Chicago, depending on variables such as the size and weight of the warhead that would be carried atop such a missile in an actual attack.
In response to the North Korean launch, the US and South Korea conducted a live-fire exercise, Pentagon said in a statement.
It said the exercise used missiles that were fired into the "territorial waters of South Korea along the East Coast".
China meanwhile, North Korea's most important ally, urged Pyongyang to abide by the relevant UN Security Council resolutions and refrain from escalating tensions, according to a foreign ministry spokesman quoted by the Xinhua news agency .
A '45-minute flight'
Earlier on Friday, the Associated Press news agency, quoting the Japanese chief cabinet secretary, Yoshihide Suga, said the North Korean missile "flew for about 45 minutes and appeared to have landed in the waters of Japan's exclusive economic zone".
The distance of the missile flight could have been more than 3,000km, Japan's NHK said, quoting a defence official.
There were no immediate reports of damage.
The Korean Central News Agency said that North Korean leader Kim Jong Un expressed on Saturday "great satisfaction" after the Hwasong-14 missile, which the country first launched on July 4, reached a maximum height of 3,725 kilometres and travelled 998 kilometres from the launch point before landing in waters near Japan.
The agency quoted Kim as saying that the latest launch reaffirmed the reliability of the country's ICBM system and confirmed an ability to launch the missile at "random regions and locations at random times" with the "entire" US mainland now within range.
Kim said the launch late Friday sent a "serious warning" to the US, which has been "meaninglessly blowing its trumpet" with threats of war and stronger sanctions, the KCNA said.
The US military and South Korea had in recent days warned that North Korea appeared to be preparing for another missile test - possibly of an ICBM or else an intermediate-range rocket.
Al Jazeera's Kathy Novak, reporting from Seoul, said Friday's apparent missile launch was "not entirely unexpected".
"There were signs from officials in the United States and South Korea that preparations were being made for a missile launch in North Korea and that the Korean Peninsula was a high alert," she said.
She also said Thursday marked the anniversary of the end of the Korean War, and "in the past North Korea has been known to take these proactive measures on important holidays".
North Korea created a stir on July 4 when it test-fired its first ICBM, a Hwasong-14 missile, which experts believe could have the potential to reach Alaska.
North Korean leader Kim Jong-un, who personally oversaw that launch on America's Independence Day, described it as a gift to the "American bastards".
North Korea is not believed to have yet developed the technology to miniaturise a nuclear weapon to fit in a missile's warhead.
Tougher measures sought
The US launched a push at the UN for tougher measures against North Korea.
In all, six sets of UN sanctions have been imposed on North Korea since it first tested an atomic device in 2006, but two resolutions adopted last year significantly toughened the sanctions regime.
Al Jazeera's Patty Culhane, reporting from Washington, DC, said the concern is that the North Korean missile fired on Friday may have been another ICBM.
"What the Pentagon is doing now is looking at the trajectory and trying to figure out how capable this missile is," she said.
Incidentally, the US military is preparing to conduct another test of a missile-intercept system in Alaska, perhaps as soon as Saturday.
That test of the Terminal High Altitude Area Defence (THAAD) system had been scheduled before Friday's developments.
The US has layers of missile defence capabilities comprising several components designed to take down different types of missile at different phases of flight.
Source: Reuters news agency