"We detected two projectiles presumed to be cruise missiles fired from the North's western port county of Onchon early Sunday", a JCS officer told reporters as quoted by South Korea's Yonhap news agency.
The officer declined to disclose any details, including the exact type of the missiles, their flight range and apogee.
The media outlet recalled, citing the South Korean military, that, unlike ballistic missiles, cruise missiles are not banned under UN Security Council resolutions on North Korea.
A senior US administration official said in earlier remarks that the United States was aware of the recent launches of short-range missiles by North Korea, but did not consider Pyongyang's actions to be provocative behaviour.
US media had reported that North Korea tested several short-range missiles over the weekend. The reason for North Korea to do so may have been the joint US-South Korea military exercises that Pyongyang had repeatedly complained about, media reports said citing sources familiar with the issue.