"The North fired two missiles into the East Sea (Sea of Japan) at about 5:00 am from the country's east coast," a defence ministry spokesman told AFP.
He declined to elaborate on the type of the missile. But Yonhap news agency, citing a military official, said they were short-range Scud missiles with a range of about 500 kilometres (300 miles).
The latest launch came after Pyongyang fired what were believed to be three short-range missiles into the sea on Thursday in an apparent show of force ahead of a visit to Seoul by Chinese President Xi Jinping.
The July 3-4 state visit marks the first time in almost two decades for a sitting Chinese president to visit South Korea before having been to the North.
China is the isolated North's sole major ally and major economic lifeline.
The North has often launched short-range missiles or rockets to express anger at perceived provocations, including military drills held south of border.
In March, it conducted multiple launches of Scud missiles and rockets to coincide with annual joint army drills between Seoul and Washington.