The "multiple projectiles" fired from Munchon in eastern Kangwon province were believed to be "surface-to-ship cruise missiles," the JCS said in a statement cited by Al Jazeera.
The missiles flew for approximately 150 kilometres (93 miles) before splashing into the waters off the east coast.
The launches come on the eve of the birthday of North Korea's founder Kim Il Sung and South Korea's general elections.
The JCS said South Korea's military is monitoring possible additional launches by North Korea.
In recent weeks, North Korea has carried out a series of short-range missile and other weapons tests amid stalled nuclear talks with the United States.
Last month, it fired nine ballistic missiles in four rounds of tests, according to analysts.
On Sunday, North Korean state media reported leader Kim Jong Un had visited an airbase and observed drills by the country's fighter jets and attack aircraft.
The North has been subjected to multiple UN Security Council sanctions over its banned weapons programs.
( With inputs from ANI )