On Tuesday the defence ministry said troops had opened fire when an unidentified flying object entered the country's airspace across the tense border with North Korea, with a military official saying it appeared to be a drone.
Defence ministry spokesman Moon Sang-Gyun on Wednesday told journalists that detailed examinations pointed to "balloon-like objects", 10 of which were observed flying with the winds in the border area. Some of them travelled into the South's territory, he said.
But Moon ruled out the possibility of the balloons coming from the South, saying that both Seoul and the southern-based activists use cylindrical balloons, rather than spherical.
Lee Min-Bok, a North Korean defector-turned-activist, told AFP that cylindrical balloons made of plastic cost much less than round rubber ones.
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"If the suspected balloons were spherical, then I suspect they were from North Korea", he said.
Tensions are high in the region over the nuclear-armed North's weapons ambitions.
South Korea has repeatedly accused the North of flying suspected spy drones across the tense border.