The missile was fired shortly before midnight Japan time on Friday, Japan's public broadcaster, NHK, said, citing government officials. Abe is convening an emergency meeting of officials, Reuters reported.
"We detected a launch of a ballistic missile from North Korea," Pentagon spokesman Lt. Col. Christopher Logan told CNBC in an email statement. "We are assessing and will have more information soon."
Japan's chief cabinet secretary, Yoshihide Suga, said the North Korean missile flew for about 45 minutes before landing in Japan's exclusive economic zone, which stretches some 200 nautical miles from its coast. Suga reported that there were no immediate reports of damage from the missile.
A South Korean military official told NBC News that North Korea fired "one unidentified projectile" into the East Sea, which is a portion of the Sea of Japan. The military official said the incident was immediately reported to South Korean President Moon Jae-in.
Top U.S. and South Korean military officials met to discuss military options after the launch, a spokesman for a top U.S. general told Reuters. Marine General Joseph Dunford and U.S. Pacific Commander Admiral Harry Harris called South Korean Joint Chief of Staff General Lee Sun-jin to discuss the commitment of the alliance and military response options.
The missile was fired from Jagang province in northern North Korea, South Korea's Yonhap news agency reported, citing the South Korean Joint Chiefs of Staff. The agency also said the South Korean president arranged an urgent meeting of his national security team.
There were indications earlier this week that nuclear-armed North Korea was preparing for another ballistic missile test. And some experts had predicted the communist nation would launch the test on Thursday to mark Victory Day, a military holiday.
Regardless, the new test represents a setback in efforts to reduce tensions on the Korean Peninsula. China, North Korea's longtime ally, has been pressuring the regime to abandon its nuclear and ballistic missile programs but so far has little to show for it.
Experts say North Korea currently is known to have the capability to send missiles to all of South Korea, Japan, as well as to Guam. And the July 4 test-firing of its first intercontinental ballistic missile indicated the regime also might be capable of striking the U.S. mainland too.
"In all honesty, we should not be surprised anymore: North Korea is slowly morphing into a nuclear and missile power right before our very eyes," said Harry Kazianis, director of defense studies at the Center for the National Interest, a think-tank founded by former President Richard Nixon.
This latest missile firing by North Korea comes a day before the U.S. prepares to conduct a new experimental test of its THAAD (Terminal High Altitude Area Defense) anti-missile defense system.
The U.S. Missile Defense Agency said earlier this week that it the THAAD test would be conducted from the Pacific Spaceport Complex in Alaska. The missile agency didn't provide details on the timing but a notice to mariners issued by the U.S. Coast Guard suggested it would likely take place Saturday evening (Alaska time) and added that alternative launch times were Sunday and Monday.
At present, two THAAD anti-missile batteries are deployed in South Korea to defend against the North's short- and medium-term ballistic missiles. The U.S.-provided system has been controversial since some claim it could be overwhelmed by a swam-like attack from the Pyongyang regime.
Also, the Chinese are upset with the Lockheed Martin-manufactured THAAD system. China claims THAAD's powerful radar gives the U.S. and South Korea capability not only to spot missiles fired from North Korea but to peer deep inside China and monitor military activities. Russia also is upset over the deployment of THAAD in South Korea.
There have been several missile tests fired this year by the North Koreans that have splashed into waters off Japan. There are currently several advanced missile defense systems protecting Japan, including a fleet of Aegis-equipped destroyers along with the Patriot PAC-3 missile system.
— Reuters contributed to this report.