The item was fired from North Pyongan province "around 7:36 am" (local time), the ministry said in a statement adding it landed in the East Sea, also known as the Sea of Japan.
The South's Yonhap news agency cited an unnamed ministry official as saying the projectile could be an intercontinental ballistic missile capable of reaching the US mainland.
Seoul and Washington launched annual joint military exercises last week that regularly infuriate Pyongyang, which condemns them as provocative rehearsals for invasion.
North Korea fired a ballistic missile last month -- its first such launch since October -- which Seoul had said was aimed at drawing "global attention" to its nuclear and missile programme and "testing the response from the new US administration" of President Donald Trump.
North Korea is barred under UN resolutions from any use of ballistic missile technology. But six sets of UN sanctions since Pyongyang's first nuclear test in 2006 have failed to halt its drive for what it insists are defensive weapons.
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