The military is analyzing the direction of the missile's flight, its range and other details.
This launch of a ballistic missile by Pyongyang was the first this year and occurred two months after the launch of a short-range ballistic missile (SRBM) on November 5, the agency noted.
The missile, presumably fired by North Korea, fell outside Japan's exclusive economic zone, the Kyodo news agency reported, citing a government source.
The source also said that no damage to Japan had been detected from the launch.
Japan's Maritime Safety Service earlier confirmed that North Korea had presumably launched a ballistic missile. Six minutes later, the service issued a message that the missile had already fallen and called on ships to report any fragments they found, but not to approach them.