The balloons carried toilet paper, batteries and suspected poo into two border provinces.
Photographs shared on social media show bags attached via string to white translucent balloons carrying toilet paper, dark soil, and batteries, among other contents.
Police and military officers are seen in some of these photographs.
South Korea's Yonhap news agency reported that "some of the fallen balloons carried what appears to be faeces judging from its dark colour and odour".
South Korea's military condemned the act as a "clear violation of international law".
"It seriously threatens the safety of our people. North Korea is entirely liable for what happens due to the balloons and we sternly warn North Korea to immediately stop this inhumane and crass action," the military said.
It does not help South Korea when they make silly statements like this.
A public health hazard is definitely a different league than inhumane and act of war. It's a little silly if anything, considering the large number And long history of pamphlets sent North from the South.