The JCS said the missile was launched at around 5:30 a.m. from an area near Pyongyang, but it is "believed to have failed."
The South Korean and U.S. intelligence authorities are conducting further analysis.
The missile launch follows Pyongyang's series of provocations including sending propaganda balloons filled with trash and feces across the border areas since late last month.
North Korea has launched a bizarre campaign of sending hundreds of such trash-filled balloons towards South Korea six times already this year, including another 250 overnight.
The JCS said no harmful substances were found in the retrieved balloons, but there are growing concerns about the safety of residents in border areas where these balloons land.
They also affected air traffic, casing disruptions and delays in landings and takeoffs at Incheon International Airport for about three hours on the same day.