The ministry provided few details of the launch, which comes as the two Koreas trade threats amid Pyongyang's anger over annual South Korean-US military drills that North Korea calls a rehearsal for an invasion.
Leader Kim Jong Un is also preparing for a major ruling party meeting next month that analysts believe he will use to further solidify his autocratic rule.
The North has fired a slew of missiles and artillery shells into the sea in an apparent protest against the drills.
The North's launch came amid speculation in the South that its rival was preparing to test a medium-range missile with a range of 3,500 kilometres enough to reach US military installments in Japan and Guam. Foreign experts have nicknamed the missile "Musudan" after the village in the northeast where North Korea has a Launchpad.
Today is the birthday anniversary of Kim Il Sung, the current leader's grandfather and the nation's founder. North Korea has occasionally used such celebrations to stage nuclear or missile tests that outsiders consider provocations.