The two missiles were fired off the east coast into the Sea of Japan, Yonhap said.
It followed a similar test-firing of four short-range Scud missiles on Thursday just days after South Korea and the United States launched their annual joint military exercises.
According to the South's defence ministry, Thursday's tests were of Scud-type missiles at the longer edge of the short-range spectrum, with an estimated reach of 300-800 kilometres -- capable of striking any target in the South.
It is not unusual for North Korea to carry out such tests -- especially to register its displeasure at the annual military drills -- and they often go unreported by South Korea.
Washington had initially played down Thursday's firings, but later suggested they violated UN sanctions imposed on the North's missile programme.
Two UN Security Council resolutions prohibit North Korea "from launching any ballistic missile, and this includes any Scud missile", Pentagon spokesman Colonel Steven Warren said Friday.