The launches, the third round of missile launches in a week, were fired off separately from North Korea's eastern coast early Friday, South Korea's Joint Chiefs of Staff told Yonhap.
The nuclear-armed North described an earlier missile launch as a warning to the South over planned joint military drills with the United States.
The projectiles were fired in the pre-dawn hours from Yonghung, South Hamgyong Province, into the East Sea, the JCS told Yonhap.
The nuclear-armed North is banned from ballistic missile launches under UN Security Council resolutions.
There was no immediate comment from Pyongyang on the latest launch.
As North Korea carried out its third weapons test in eight days Friday, according to the South's military, but US President Donald Trump said he had "no problem" with the spate of launches by Pyongyang.
The nuclear-armed North is barred from ballistic missile tests under UN resolutions and its actions have drawn condemnation from European members of the Security Council but a comparatively sanguine response from Trump, who has met North Korean leader Kim Jong Un three times, generating global headlines on each occasion.
"I have no problem. We'll see what happens but short range (missiles) are very standard," Trump told reporters as he left the White House for a rally in Ohio.
Kim and Trump agreed to resume denuclearisation talks during their impromptu June encounter in the Demilitarised Zone(DMZ) that divides the peninsula, but that working-level dialogue has yet to begin.