Ministry spokesman Kim Min-Seok said a joint investigation with US experts of recovered data from the unmanned aerial vehicles (UAVs) showed they had been pre-programmed to fly over South Korean military installations and then return to the North.
"By analysing the data, the joint investigation team has secured the smoking gun -- clear, scientific evidence that all three UAVs originated from North Korea," Kim said.
"This is a clear military provocation," he added.
One crashed due to an engine problem, while the other two ran out of fuel.
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"All three had been programmed to fly over our military facilities, Kim said, describing the drone incursions as "a new type" of military threat that required a "stern" response.
In a separate briefing with foreign journalists, Vice Defence Minister Baek Seung-Joo said the drones were unsophisticated UAVs with no live ground-control system and rudimentary programming systems.
"However, there is always the possibility that the North might use them for attacks after arming them with high explosives, considering its irrational and reckless tendency for provocative acts," Baek said.
All three UAVs were equipped with cameras and had taken pictures of border areas and the capital Seoul, including the presidential palace.
North Korea had displayed a set of what looked like very basic drones during a huge military parade held in Pyongyang last July to mark the 60th anniversary of the end of the Korean War.