Alleged launch came after Washington and Seoul deployed an advanced missile system in the South.
North Korea fired a submarine-launched ballistic missile on Saturday but the launch appears to have failed in the early stages of flight, South Korea's military said.
The launch came a day after the US and South Korea pledged to deploy an anti-missile system and two days after North Korea warned it was planning a tough response to what it called a "declaration of war" from the United States.
That followed Washington slapping sanctions on the nation's leader Kim Jong Un.
The South's Joint Chiefs of Staff said in a statement that the missile was launched at about 1130am Seoul time (0230GMT) in waters east of the Korean peninsula.
MWC News could not indepedently verify the launch.
The missile was likely fired from the submarine as planned but appears to have failed in the early stage of flight, the Joint Chiefs of Staff said.
'Means for attack'
The North has conducted a string of military tests that began in January with its fourth nuclear test and included the launch of a long-range rocket the next month.
The UN Security Council imposed harsh new sanctions on the country in response to North Korea's fourth nuclear test and the long-range rocket.
South Korea and the United States said on Friday they would deploy an advanced missile defence system in South Korea, drawing a sharp and swift protest from neighbouring China, Pyongyang's sole major ally.
Pyongyang also conducted a test of a submarine-launched ballistic missile (SLBM) in April, calling it a "great success" that provided "one more means for powerful nuclear attack".
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