Seoul warned the public on Saturday to avoid more balloons sent from North Korea and to report them to the military or police.
South Korea's military said North Korea was sending more balloons carrying "filth" across the heavily fortified border.
North Korea sent hundreds of balloons carrying trash and excrement earlier this week, calling them "gifts of sincerity" and vowing to send more. South Korean Defence Minister Shin Won-sik on Saturday called this "unimaginably petty and low-grade bahaviour".
A public message broadcasted by the city of Seoul asked the public to refrain from touching balloons "identified in the sky near Seoul" and to report them as these were "being handled by the military".
Other regional governments had been asked to broadcast similar messages, the defence ministry said.
North Korea has said the balloons were retaliation for an ongoing propaganda campaign by North Korean defectors and activists in South Korea, who send balloons containing anti-Pyongyang leaflets, food, medicine, money and USB sticks loaded with K-pop music videos and dramas across the border.