SEOUL — North Korea on Tuesday fired an intermediate-range ballistic missile over Japan for the first time in five years, prompting a rare warning by the Japanese government for residents in two northern prefectures to seek shelter.

The launch represented a major escalation by North Korea, which has conducted a flurry of missile tests in recent days as the United States held military drills in the region with South Korea and Japan. By launching a missile over Japan and toward the Pacific, North Korea heightened regional concerns over its growing nuclear capabilities, and raised the stakes in stalled diplomatic talks with Washington.

The intermediate-range missile was fired from Mupyong-ri, near North Korea’s central border with China, according to the South Korean military. It was launched at 7:22 a.m. and landed in the Pacific Ocean 22 minutes later, Japan’s chief cabinet minister, Hirokazu Matsuno, said. It crashed about 1,864 miles — or 3,000 kilometers — east of the archipelago, outside Japan’s exclusive economic zone, which extends 200 nautical miles from its shores.

The test was seen as a direct challenge to South Korea’s effort to strengthen its alliance with the United States and improve ties with Japan, a former colonial ruler of Korea with longstanding historical disputes with Seoul. The missile flew about 2,800 miles, the longest distance ever traveled by a North Korean missile, officials in Tokyo and Seoul said.

Although North Korea has developed and tested increasingly powerful ballistic missiles in recent years, it has rarely fired them over Japan, an act considered extremely provocative by both Tokyo and Washington. Instead, North Korea has usually launched its missiles at a deliberately steep angle, with the projectile soaring high into space before falling into waters west of Japan.

North Korea has only fired missiles over Japan twice before, both times in 2017.

Adrienne Watson, a spokeswoman for the White House’s National Security Council, called the launch a “dangerous and reckless decision.” Unlike the South Korean government, she described the North Korean weapon as “a long-range ballistic missile.” National Security Adviser Jake Sullivan spoke with his Japanese and South Korean counterparts on Tuesday to discuss “robust joint and international responses” and reinforced Washington’s “ironclad commitments” to the defense of its allies, Ms. Watson said.

North Korea has insisted that it was building a nuclear arsenal for self-defense, accusing the United States and its allies of plotting to invade the isolated country. In a speech to Parliament last month, Kim Jong-un, the North’s leader, said his country would never give up its nuclear weapons “as long as the United States and its vassal forces refuse to stop their anti-D.P.R.K. maneuverings.” (D.P.R.K. stands for the Democratic People’s Republic of Korea, the North’s official name.)

President Yoon Suk Yeol of South Korea met with Japanese Prime Minister Fumio Kishida in New York last month on the sidelines of the United Nations General Assembly. The two leaders discussed security cooperation in the face of North Korea’s growing nuclear and missile threat. In recent weeks, the United States, Japan and South Korea have conducted their first trilateral anti-submarine and missile-tracking exercises since 2017.

North Korea has fired 23 weapons tests this year that involved a total of 43 ballistic and cruise missiles — including four tests last week — but the launch on Tuesday was the first time since 2017 that Japan had issued a warning for residents to take shelter.

The Japanese government urged people in the prefectures of Aomori and Hokkaido, as well as several islands near Tokyo, to seek shelter while it tracked the path of the missile.

“North Korea’s continuous provocations will not be ignored and we make it clear that it will have to pay a price for them,” Mr. Yoon’s office said on Tuesday after a meeting with his National Security Council. The South Korean president said Seoul would work with Washington to strengthen the sanctions against North Korea.

Mr. Matsuno, the Japanese cabinet minister, said in a morning news briefing that North Korea’s actions, “threaten the peace and security of our region and the international community,” adding that Japan condemned the launch “in the strongest possible terms.”

North Korea launched a three-stage rocket over Japan in 1998 and again in 2009. In both cases, the country claimed that it was launching a satellite into orbit, but Washington accused the country of using its space rocket program to develop long-range ballistic missile technology.

The last time a North Korean missile flew over Japan was on Sept. 15, 2017, when the country launched its intermediate-range ballistic missile, the Hwasong-12. The missile flew 2,300 miles, crashing into waters 1,370 miles east of Hokkaido, the northernmost main Japanese island.

North Korea and the United States seemed as though they were edging toward conflict in 2017. Mr. Kim and President Donald J. Trump exchanged personal insults and threats of war, including Mr. Trump’s vow to unleash “fire and fury.”

The 2017 Hwasong-12 tests followed a threat by North Korea to launch four intermediate-range ballistic missiles into waters around Guam, a United States territory in the Western Pacific which would serve as a launchpad for American reinforcements in case of war on the Korean Peninsula.

The range of the missile launched on Tuesday was enough to reach Guam.

“Through this latest test, North Korea is proving that they were not empty words when it said it was boosting its nuclear force,” Yang Moo-jin, a professor at the University of North Korean Studies in Seoul, said.

This year, the United States revived large-scale joint military drills with South Korea, dispatching the American aircraft carrier U.S.S. Ronald Reagan to waters off the east coast of the Korean Peninsula in September. In his Armed Forces Day speech on Saturday, Mr. Yoon said South Korea and the United States were discussing bolstering their joint deterrence against North Korea, including a timely deployment of nuclear-capable American war ships and war planes.

He warned that if North Korea attempts to use a nuclear weapon, “it will face a resolute and overwhelming reaction from the South Korea-United States alliance and our military.”

For months, Washington and Seoul have warned that North Korea was preparing for another nuclear test at Punggye-ri, where the North has conducted all of its six previous underground nuclear tests. Under multiple resolutions by the United Nations Security Council, North Korea is banned from developing or testing ballistic missiles, as well as nuclear weapons.

Choe Sang-Hun reported from Seoul and Motoko Rich from Tokyo. Hikari Hida contributed reporting from Tokyo.