The rubbish that fell on the ground at the compound in central Seoul on Wednesday contained no dangerous material and no one was hurt, South Korea's presidential security service said.
While North Korea likely lacks sophisticated technology to drop balloons on specific targets, some experts say South Korea should shoot down incoming North Korean balloons to protect key facilities despite the prospect of increased tensions or damage on the ground, as they might contain dangerous substances in future campaigns.
North Korea's latest launches came days after South Korea boosted its frontline broadcasts of K-pop songs and propaganda messages across the rivals' heavily armed border.
Their tit-for-tat, Cold War-style campaigns are inflaming tensions, with the rivals threatening stronger steps and warning of grave consequences.
Seoul officials earlier said North Korea had used the direction of winds to fly balloons towards South Korea, but some of the past balloons had timers that were likely meant to pop the bags of rubbish midair.
The security service gave no further details about the rubbish found at the presidential compound.
It refused to disclose whether President Yoon Suk-yeol was at the compound when North Korean balloons were flying over his office.
If North Korea is found to have used timers or any other device to deliberately dump trash on the presidential office, it would certainly invite a strong response by South Korea.
But experts say dropping balloons on ground targets requires advanced technology and that North Korea would certainly lack such an ability.
South Korea's Joint Chiefs of Staff said earlier on Wednesday that North Korea had restarted floating balloons across the border, the 10th such launch since late May.
The more than 2000 North Korean balloons discovered in South Korea in the past weeks carried wastepaper, scraps of cloth, cigarette butts and even manure.
North Korea has said it was responding to South Korean activists scattering political leaflets across the border via their own balloons.
The North's balloons have not caused major damage but have raised security jitters among people worried North Korea could use such balloons to drop chemical and biological agents.
South Korea has avoided shooting at balloons citing concerns about damages and the possibility they might contain hazardous substances.
Experts say North Korea considers South Korean civilian leafleting activities a major threat to its efforts to stop the inflow of foreign news and maintain its authoritarian rule.
South Korea said on Sunday it was ramping up its anti-Pyongyang propaganda broadcasts from its loudspeakers along the land border because North Korea was continuing launches of rubbish-carrying balloons.
South Korea last Thursday restarted its loudspeaker broadcasts for the first time in about 40 days in retaliation for North Korea's previous balloon activities.
