Launches by the North of short-range missiles are not uncommon but, after recent warnings from the communist state of impending nuclear war, such actions have raised concerns about the region's security.
"North Korea fired a short-range missile as it did yesterday into its east sea in the afternoon, " South Korea's news agency Yonhap reported, citing a military official.
A South Korean defense ministry official confirmed the Yonhap report, but did not provide any details.
U.N. Secretary General Ban Ki-moon said he was concerned about North Korea's launch of short-range missiles, urging Pyonyang to refrain from further launches and return to stalled nuclear talks with world powers.
Ban, who spoke to Russian state news agency RIA Novosti during a visit to Moscow, called Saturday's launch a "provocative action".
Tension on the Korean peninsula has subsided in the past month, having run high for several weeks after the United Nations Security Council imposed tougher sanctions against Pyongyang following its third nuclear test in February.
The North had for weeks issued nearly daily warnings of impending nuclear war with the South and the United States.
South Korea's Unification Ministry criticized the missile tests as deplorable and urged the North to lower tensions and hold talks over a suspended inter-Korean industrial park in the North's border city of Kaesong.
South Korea pulled out all of its workers from the industrial zone early this month after North Korea withdrew its 53,000 workers as tensions mounted.