South Korea and the U.S. conducted a joint strike package flight and precision bombing drill in response to the ballistic missile test, South Korea's Joint Chiefs of Staff told ABC news.
The Japanese government issued a “J-alert” through its emergency warning system, advising residents to take cover in sturdy buildings or underground.
A government spokesperson said Japan didn’t attempt to shoot the missile down because they didn’t think it posed a threat.
A U.S. defense official confirmed the launch to ABC News.
Residents in Aomori and Hokkaido prefectures, toward the northern end of Japan, were advised to be on alert and to notify police or fire officials if debris is seen.
Tuesday's launch marked the seventh time a North Korean missile flew over Japan. The last time was in August 2017. North Korea has shot 21 ballistic missiles and two cruise missiles since January, a record-breaking number of launches in a single year. Tuesday's launch was the country's fifth missile test in just over a week.
“We ask that people return to life as usual, calmly," the Japanese government’s chief spokesman Hirokazu Matsuno told reporters at a press conference.
People were also warned by officials not to touch or pick up any debris.
The office of Japanese Prime Minister Fumio Kishida began to gather members to analyze the situation.
A government spokesperson said no damage has been reported so far and a search is underway for debris. Officials are gathering information and will work with South Korea and the U.S.
"North Korea's actions threaten Japan and the international community," the spokesperson said. "Missile launches like this go against the U.N. resolutions. Japan will launch a strong protest against North Korea in light of this. All new information will be shared promptly."
The White House said in a statement late Monday local time in Washington, D.C., that "the United States strongly condemns the Democratic People's Republic of Korea's (DPRK) dangerous and reckless decision to launch a long-range ballistic missile over Japan."
U.S. National Security Adviser Jake Sullivan spoke with his Japanese and South Korean counterparts on Monday night local time, according to White House National Security Council spokesperson Adrienne Watson.
"In both calls, the National Security Advisors consulted on appropriate and robust joint and international responses," Watson said, "and National Security Adviser Jake Sullivan reinforced the United States' ironclad commitments to the defense of Japan and the ROK [South Korea]."
Regional players may have few cards left in their hands to play towards curbing North Korea, observers said. Jeff Kingston, director of Asian Studies at Temple University Japan, told ABC News that the missile launch was a very provocative act as it comes amidst numerous missile tests this year.
“There are no good options for [South Korean President] Yoon, Kishida, Biden to rein in Kim Jong Un,” Kingston said. “Sanctions and condemnation have failed to deter him and there is no good military option.”
North Korea recently passed a law declaring its readiness to launch preemptive nuclear strikes. Analysts warned that the country may seek to reaffirm its nuclear weapons state status and is prepping for a seventh nuclear test.
Jaechun Kim, professor of international relations at South Korea's Sogang University, said the U.S., Korea and Japan should mobilize cooperation from like-minded countries in non-U.N. sanctions to thwart North Korea’s provocations.
“A unified front must be established that imposes sanctions on North Korea, as they did on Russia,” Kim said. “This is the only way to penalize North Korea for its bad behavior.”
Kim also told ABC News that China, North Korea’s strongest ally, may have no little or no say in North Korea’s actions.
“North Korea just does what it needs to do these days. So, with or without China’s support, it is quite likely for the North to conduct 7th nuke test,” Kim said. “It will be interesting to see whether Xi Jinping will throw his weight behind Kim Jong Un.”
ABC News' Joohee Cho, Guy Davies and Matt Seyler contributed to this report.