One missile was fired from the eastern city of Wonsan at 5:20 a.m., the South Korea Joint Chiefs of Staff (JCS) said.
"Our military has maintained readiness as (we are) bracing for possibilities of additional provocations," said Jeon Ha-gyu, the chief of public affairs for the JCS.
It appears to be the latest in a string of missile tests as the country tries to advance its weapons program in defiance of the international community and its closest regional ally, China.
Local media reports suggested it was a medium-range Musudan missile; if confirmed, it would be the fourth time North Korea has tried and failed to launch this type of missile.
Yoshihide Suga, Japan's chief cabinet secretary, said that no missile was confirmed to have flown towards Japan.
The last several months have been particularly contentious on the Korean Peninsula, after North Korea claimed to have testedits first hydrogen bomb and fired a satellite into orbit. Both actions violated numerous United Nations Security Council resolutions.
Earlier this month, North Korean leader Kim Jong Un proposed holding military talks with South Korea to ease tensions but Seoul dismissed the offer, saying it wasn't sincere given that Pyongyang was continuing to develop a nuclear arsenal.
CNN