It described the weapons as strategic, implying an intent to arm them with nuclear warheads, but did not specify whether they were launched from an actual submarine or an underwater test platform.
A ministry statement said that South Korea will continue consultations with Ukraine, adding it hopes the dispute between the two countries would be resolved smoothly.
The announcement came days after North Korea denied responsibility for the Sept. 21 blasts and threatened "merciless" retaliation if provoked over the case.
North Korea's military has laid mines and built anti-tank barriers along the frontier as part of efforts to permanently seal it off following leader Kim Jong Un's designation of South Korea.
