South Korean President Moon Jae-in has been briefed on the latest launch, the military said, declining to give further details.
"North Korea launched multiple projectiles that appear to be short-range land-to-ship cruise missiles today morning off east coast from the region of Wonsan," the office said in a statement, adding that Seoul and Washington were analysing the launches for further information.
Thursday's launch is the fourth missile test by North Korea since Moon took office on May 10 pledging to engage in dialogue with Pyongyang, saying sanctions and pressure alone have failed to resolve the growing threat from the North's advancing nuclear and missile programme.
South Korea said on Wednesday it will hold off on installing remaining components of a controversial US anti-missile defense system until it completes an assessment of the system's impact on the environment.
Under third-generation leader Kim Jong Un, North Korea has been conducting such tests at an unprecedented pace in an effort to develop an intercontinental ballistic missile (ICBM) capable of hitting the mainland United States.
In the three earlier launches, North Korea tested different kinds of ballistic missiles, two medium-to-long range missiles as well as a short-range Scud class weapon.
The isolated country, which has conducted dozens of missile tests and tested two nuclear bombs since the beginning of 2016 in defiance of UN Security Council resolutions, says the programme is necessary to counter US aggression.
(Reporting by Ju-min Park and Soyoung Kim; Editing by Lincoln Feast)