The missiles were launched at around 12:30 p.m. (0330 GMT) from an area around Wonsan on North Korea’s eastern coast, the JCS said.
South Korea’s military was strengthening surveillance and maintaining readiness in case of additional launches, while closely sharing information with the United States and Japan, it added.
Japan’s Defense Ministry said North Korea had launched an object that could be a ballistic missile and that it fell outside Japan’s Exclusive Economic Zone, according to Yonhap News Agency.
Japan’s Coast Guard also said earlier the launched projectile could be a ballistic missile and had already fallen into the sea.
North Korea last fired ballistic missiles on October 12, amid heightened tension on the inter-Korean border over a mine blast that wounded South Korean soldiers last month.
Pyongyang has conducted missile tests on more than 10 occasions this year.