Yonhap news agency quoted a government official as saying that the missile, KN-11, was fired between 2:20 pm (05:20 GMT) and 2:40 pm.
"The North appears to have failed in its launch," said the official on condition of anonymity, according to Yonhap.
"The missile was not seen flying in the air only debris from its coverings was spotted", he said.
A South Korean defence ministry spokesman refused to comment on the report when contacted by AFP.
The missile appeared to have flown only about 100 or 150 metres (330-495 feet) from the surface of the water but South's defence ministry described the launch at the time as "very serious and worrisome".
Under UN Security Council resolutions, the nuclear armed North Korea is banned from any test using ballistic missile technology.
North and South Korea remain technically at war after a war ended in an armistice instead of a peace treaty in 1953.
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