The agency said the South's Joint Chiefs of Staff reported the missile was fired toward the East Sea, also known as the Sea of Japan, in the latest act of defiance from Pyongyang amid acute tensions with Seoul and Washington.
The South's military gave no immediate details of the launch, the agency said.
Japan confirmed the launch, with the office of Prime Minister Fumio Kishida tweeting at 1034 GMT that "North Korea launched what appears to be a ballistic missile."
Pyongyang has opened the year with a flurry of weapons tests, including what its state media has claimed are nuclear-capable underwater drones and the launch of two intercontinental ballistic missiles.
On Monday, North Korean leader Kim Jong Un attended a meeting of the Central Military Commission to discuss ways to "cope with the escalating moves of the US imperialists and the south Korean puppet traitors to unleash a war of aggression," Pyongyang's Korean Central News Agency said.
Kim ordered that the country's deterrence capabilities be strengthened with "increasing speed" and in a "more practical and offensive" manner.
North Korea last year declared itself an "irreversible" nuclear power, effectively ending the possibility of denuclearisation talks.
Earlier this year, Kim ordered the military to intensify drills to prepare for a "real war".
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