A ministry spokesman said the missile was launched from Sukchon in the country's southwest at 5:55 am (local time) and flew 800 kilometres into the East Sea, also called the Sea of Japan.
He did not confirm the type of missile, but South Korea's Yonhap news agency cited military sources as saying it was a Rodong missile, a scaled-up Scud variant with a maximum range of around 1,300 kilometres.
The UN Security Council responded earlier this month by imposing its toughest sanctions on North Korea to date.
US President Barack Obama signed an order on Wednesday implementing the UN sanctions, as well as a series of unilateral US sanctions adopted by Congress.
Pyongyang, meanwhile, has maintained a daily barrage of nuclear strike threats against both Seoul and Washington, ostensibly over ongoing, large-scale South Korea-US military drills that the North sees as provocative rehearsals for invasion.
A few days later, North Korean President Kim Jong-Un announced that a nuclear warhead explosion test and firings of "several kinds" of ballistic rockets would be carried out "in a short time".
Existing UN sanctions ban North Korea from the use of any ballistic missile test, although short-range launches tend to go unpunished.
A Rodong test would be more provocative, given its greater range which makes it capable of hitting most of Japan.
The last Rodong test was in March 2014, when two of the missiles were fired into the East Sea.
There are numerous question marks over the North's weapons delivery systems, with many experts believing it is still years from developing a working inter-continental ballistic missile (ICBM) that could strike the continental United States.
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