Korean words on batteries recovered from the unsophisticated unmanned aerial vehicle were of a type only used north of the border, a defence ministry spokesman said.
"So we suspect the vehicle was sent by North Korea," the spokesman said, adding that the drone was of an extremely "rudimentary" design.
The drone was equipped with a Japanese camera but had no ability to transmit images.
The spokesman said it had taken pictures of Seoul's northern suburbs, but declined to confirm reports that it had captured images of the presidential Blue House.
Its wreckage was discovered on Baengnyeong island, which lies just south of the maritime border, and the spokesman said it was still being analysed by military intelligence.
North Korea had displayed a set of very basic looking drones during a huge military parade held in Pyongyang last July to celebrate the 60th anniversary of the end of the Korean War.
And in March last year, state media reported leader Kim Jong-Un overseeing a military drill using "super-precision drone planes".
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