Trash carried by the balloons was identified in the area around the government complex in the Yongsan area, the security service said in a statement.
The objects in the balloons contained no contaminants or other risks, it added.
It was not clear if President Yoon Suk Yeol was in the complex on Wednesday.
Since May, North Korea has periodically sent hundreds of balloons carrying an assortment of trash across the heavily fortified border with the South, prompting South Korea's military to restart loudspeaker broadcasts targeting the North.
Ko Seok-noh, a resident of Paju, was concerned about balloons flying over the border town which is about an hour north of Seoul.
"It's uncomfortable for us when the balloons come over. It's trash coming over," Ko told Reuters.
The balloons have also caused wider disruption and last month briefly halted operations at Incheon, the world's fifth-busiest international airport and an important cargo hub.
The North has said it is retaliating to an ongoing propaganda campaign by North Korean defectors and activists in the South, who regularly send inflatable containing anti-Pyongyang leaflets, alongside food, medicine, money and USB sticks loaded with K-pop videos and dramas.
North Korea had sent another batch of trash-laden balloons earlier on Wednesday, South Korea's military confirmed.
"With the current wind direction being westerly, the suspected trash balloons aimed at the South are moving towards the northern part of Gyeonggi (province)," the Joint Chiefs of Staff (JUS) said.
Since 2022, the presidential office in South Korea has been located in Yongsan, a central district in Seoul, after President Yoon broke with decades of tradition and moved out of the more secluded Blue House.
