Tokyo (CNN) US President Donald Trump has warned Pyongyang that "all options are on the table" after North Korea fired a missile over Japan early Tuesday.

Tuesday's launch was particularly provocative as it was North Korea's first ballistic missile to fly over Japan. Kim Jong Un's regime regularly fires missiles into the sea between its own territory and Japan.

On Wednesday morning local time the official North Korean news agency, KCNA, acknowledged the missile launch reporting that the North Korean leader guided the launch of the Hwasong-12 intermediate-range ballistic missile over Japan.

Officials summarized the media reports to CNN in Pyongyang, saying the launch was overseen by Kim Jong Un who was "very satisfied with the performance of the missile."

They said the launch was a strong message in response to the ongoing joint US-South Korean military exercise in the southern half of the Korean peninsula. They added the launch was the first of its kind into the Pacific Ocean and was a prelude to more military options aimed at Guam with more launches planned in the future. It was also carried out on the 107th anniversary of the annexation of Korea by Japan in 1907.

"Initial assessment indicates the launch of an intermediate range ballistic missile," according to a Pentagon statement released on Tuesday.

"The launch occurred in the vicinity of Sunan Air Base, North Korea and flew east ... The ballistic missile overflew the territory of northern Japan before landing in the Pacific Ocean approximately 500 nautical miles east of Japan," the statement said.

The launch comes as the US and South Korea conduct joint military drills on the peninsula and a day after drills ended between the US and Japan on the northern island of Hokkaido

It also follows a fiery exchange of threats and insults between Trump and the North Korean regime, commenting through state media.

"The world has received North Korea's latest message loud and clear: this regime has signaled its contempt for its neighbors, for all members of the United Nations, and for minimum standards of acceptable international behavior," Trump said in a statement, taking a more measured tone than in his previous remarks.

"Threatening and destabilizing actions only increase the North Korean regime's isolation in the region and among all nations of the world. All options are on the table."

Minutes after the missile was launched, residents in northern Japan received a text message urging them to seek shelter in a strong structure or a basement.

"We were awoken by sirens and messages from the government telling us to take cover," one local resident told CNN.

Japanese Prime Minister Shinzo Abe -- who had a 40-minute phone call with Trump on Tuesday -- described the launch as a "reckless act."

"This launch of a North Korean missile is an unprecedented serious and grave threat to Japan," Abe said after the call, adding that Trump said "the US stands with Japan 100%."

"I would like to make the utmost effort to protect the lives and assets of the Japanese people under a strong alliance between Japan and US."

What happened?

The missile was fired just before 6 a.m. Japan time (Monday 5 p.m. ET), and the launch set off warnings in the northern part of the country urging people to seek shelter.

The unidentified missile flew over Erimomisaki, on the northern island of Hokkaido, and broke into three pieces before falling into the Pacific Ocean, about 1,180 kilometers (733 miles) off the Japanese coast.

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The missile was in flight for about 15 minutes, Chief Cabinet Secretary Yoshihide Suga said at an emergency press conference.

"There is no immediate report of the fallen objects and no damage to the ships and aircraft," he said.

News had still not been broadcast to people in North Korea by Tuesday evening in Pyongyang.

The missile was fired from a location near Pyongyang, in a provocative and rare move by the regime. It may have been intended to deliver a message that pre-emptive US strikes on missile launch facilities could land uncomfortably close to civilians.

It was the fourth missile North Korea fired in four days -- Pyongyang tested three short-range ballistic missiles , one of which failed, from Kangwon province that landed in water off the Korean Peninsula.

South Korea responded by conducting a bombing drill at 9:30 a.m. local time to test its "capability to destroy the North Korean leadership" in cases of emergency, an official with the country's Defense Ministry told CNN.

Why Japan?

Tuesday's launch is the first time North Korea has successfully fired a ballistic missile over Japan. Various stages of launch vehicles have overflown Japan during Pyongang's attempts to launch satellites into space in 1998, 2009 2012 and 2016

While the missile flew over Japanese territory, one analyst said it wasn't necessarily intended as a threat to the country.

"If they're going to launch to a distance they've got to go over somebody. It looks to me like a risk reduction measure, they want to reduce the populated areas they fly over just in case anything goes wrong," said Joshua Pollack, a senior research associate at the James Martin Center for Nonproliferation Studies.

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The launch also comes just over two weeks after North Korea threatened to fire a series of missiles in the waters around the US Pacific territory of Guam.

The country has not followed through with that threat, but firing a missile over Japan and into the Pacific is in Guam's direction, even if nowhere near the island.

David Wright, co-director of the Global Security Program at the Union of Concerned Scientists, told CNN that Tuesday's launch shows a new level of confidence from the North Koreans.

"It is a big deal that they overflew Japan, which they have carefully avoided doing for a number of years," he said.

He added that the country had in the past tested missiles upwards on high trajectories and launched their satellites to the south to avoid firing missiles over Japan.