The missiles were launched from a base on the west coast and flew more than 100 kilometres, the spokesman for the South's joint chiefs of staff told AFP.
"The missile test launch, which lasted 45 minutes from 4:15 pm, appeared to have been supervised by Kim Jong-Un," he said, adding that the exact model of the projectiles was not known.
The exercise came at a time of elevated tensions with North Korea's condemnation of annual US-South Korea military drills that Pyongyang views as rehearsals for invasion.
The annual exercises always trigger a surge in military tensions between the two Koreas, who remain technically at war because the 1950-53 Korean conflict ended with a ceasefire rather than a peace treaty.
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Seoul and Washington insist the exercises are defence-based in nature, but they are regularly condemned by Pyongyang as provocative rehearsals for invasion.
North Korea signalled its displeasure when this year's drills began in early March by firing two short-range ballistic missiles into the sea off its east coast.
Today's launch came a day after North Korea test-fired a short-range missile from the same base in Dongchang-ri, a rocket launching site close to the northern border with China, the South Korean military spokesman said.
The Dongchang-ri site is bigger than the Musudan-ri site on the east coast where the North has launched long-range missiles.
UN resolutions ban any ballistic missile test by North Korea.
The nuclear-armed country has pushed ahead with the development of ballistic missiles and rockets, despite tough sanctions imposed by the international community.