Launch comes days after North Korea test-fired a suspected ICBM into the Sea of Japan.
The JSC did not immediately provide specifics on Sunday’s launch.
The Japan Coast Guard also said what was fired by North Korea could be a ballistic missile.
The launch comes after North Korea fired a suspected intercontinental ballistic missile (ICBM) into the sea between the Korean peninsula and Japan on Thursday, hours before South Korea’s president flew to Tokyo for a summit that discussed ways to counter their nuclear-armed neighbour.
North Korean state media described the launch of the Hwasong 17 as a response to the ongoing, “frantic” joint drills by South Korea and the United States.
Seoul and Washington have ramped up security cooperation after a year of record-breaking North Korean weapons tests and nuclear threats.
Pyongyang views all such exercises as rehearsals for invasion.
Last year, North Korea declared itself an “irreversible” nuclear power, and leader Kim Jong Un recently called for an “exponential” increase in weapons production, including tactical nuclear weapons.