A drone, which had been photographing a controversial US missile defence shield, was discovered early June after it crashed close to a sensitive military installation along the heavily fortified border, Seoul's military said.
"The latest action by the North... Is a grave provocation and a wanton violation of the armistice," Jeon Dong-Jin, first deputy director of the South's Joint Chief of Staff, told reporters, referring to the treaty which ended the 1950-53 war.
"We strongly condemn the North's series of drone provocations and urge it to stop all such provocations immediately," Jeon said, vowing "strong retaliation" against any further actions by Pyongyang.
The South has requested an investigation by the UN Command which is in charge of supervising the armistice, which ended open conflict between the two sides, but has never been replaced with a final peace treaty.
More From This Section
Photos retrieved from the latest drone include several overviews of the site for the Terminal High Altitude Area Defense (THAAD) system in the southeastern county of Seongju, according to the military.
The powerful US anti-missile system was installed this year to guard against growing missile threats from the nuclear-armed North.
South Korea in recent years has repeatedly accused the North of flying suspected spy drones across the tense border bisecting the peninsula.