The missile was fired just before 6 a.m. in Japan. 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,CNN reported.
The missile was in flight for about 15 minutes, Chief Cabinet Secretary Yoshihide Suga said at an emergency press conference. "There are no immediate report of the fallen objects and no damage to the ships and aircraft," he added.
Abe, who shared a 40-minute phone conversation with US President Donald Trump in response to the launch, said the two leaders had agreed to call for an immediate emergency meeting of the UN Security Council "and increase the pressure towards North Korea."
During the call, Trump reiterated that the United States "stands with Japan 100%" said Abe.
The missile was launched near the North Korean capital of Pyongyang, which is rare.
CNN's Will Ripley, who is on the ground in Pyongyang, said the news had not been broadcast to people inside North Korea as of 9:45 a.m. local time.
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.
Yoon Young-chan, the head of South Korea's Presidential Office Public Affairs Office, told reporters that four F-15K fighter jets dropped eight one-ton MK-84 bombs at a shooting range.
The operation was meant "to showcase a strong punishment capability against the North," he said.
Tuesday's launch is the first time North Korea has successfully fired a missile over Japan since 1998, when it sent a satellite launch vehicle over the country.
It also comes just three days after Pyongyang test-fired three short-range ballistic missiles from Kangwon province that landed in water off the Korean peninsula -- of the three, one failed.
Analysts believe 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, even though it forced them to test missiles on highly lofted trajectories, and forced them to launch their satellites to the south, which is less efficient than launching to the east (due to the Earth's rotational motion)," said David Wright, co-director of the Global Security Program at the Union of Concerned Scientists.
US Senator Lindsey Graham quickly weighed in on Twitter, calling the launch a "a big-time" escalation of conflict.
Graham made headlines earlier this month after telling NBC's "Today" show that President Trump assured him "if there's going to be a war to stop them, it will be over there," a comment which concerned US allies already in range of much of North Korea's arsenal.
Pyongyang's missile tests are banned under United Nations Security Council resolutions, but that hasn't stopped North Korean leader Kim Jong Un from attempting to rapidly develop his country's nuclear and missile programs.
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.
The first message came in at 6:02 a.m. Japan time:
"Missile launched. Missile launched. It seems that the missile has been launched from North Korea. Please evacuate to building with strong structure or go to the basement."
The second alert came in about 12 minutes later:
"Missile passed. Missile passed. A minute ago, the missile seems to have passed the airspace of this area. If you find anything suspicious, please don't come close to it, report to the police and firefighter directly."
The administration of US President Donald Trump is pursuing what it calls a strategy of "peaceful pressure" to rein in North Korea's weapons programs.
The goal is to put enough diplomatic and economic pressure on Pyongyang in order to push them to the negotiating table.
Last week, Secretary of State Rex Tillerson and Trump hinted that the strategy appeared to be working.
Trump mused at a rally in Phoenix that Kim might now respect the United States. At a State Department briefing Wednesday in Washington, Tillerson said the brief respite in the missile launches may have been an example of North Korea demonstrating restraint.
"If Trump and Tillerson believed North Korea backed down, they were sorely mistaken," said Adam Mount, a senior fellow at the Washington-based Center for American Progress.
"They're not going to volunteer to do this (give up their weapons). Ever," he said. "It's a matter of bargaining. And North Korea has signaled over and over again that the price is really high."
Analysts say North Korea believes developing a nuclear weapon that can fit atop a missile powerful enough to reach the United States is the only way Pyongyang can deter any US-led efforts at regime change.
"They cross line after line in an effort to say this is the new reality and you should accept it and go easy on us," Mount said. "I think that's a pretty unambiguous signal that they're no longer going to be restrained by the United States."
The launch was also likely a signal to Japan, analysts say, as it comes the day after the Northern Viper military drills ended between the United States and Japan on Hokkaido -- part of a North Korea strategy to drive a wedge between the US and its two main allies in the region -- Japan and South Korea.
Japanese Chief Cabinet Secretary Suga told reporters this launch "could endanger peace and security in the Asia-Pacific region. It is also very dangerous and problematic in terms of the traffic safety of planes and ships."
The United States is currently participating in its annual 10-day Ulchi Freedom Guardian military exercises with South Korea, which began on August 21.
Those drills are more logistical and defensive in nature -- though Pyongyang sees them as provocative -- whereas the Northern Viper drills could be considered more operational, Mount said.
South Korea's Foreign Ministry condemned the North Korean launch as "yet another provocation despite grave messages of warning," in a statement Tuesday.
"The North Korean regime needs to realize that denuclearization is the only true path to securing its security and economic development and needs to come to the path for nuclearization dialogue instead of conducting its reckless provocation," the statement said.