South Korea's Joint Chiefs of Staff said it could not confirm the North's accusations but also referred in its statement to Pyongyang's practice of sending into South Korean airspace balloons with bags of trash attached.
North Korea's foreign ministry said the drones were flown over Pyongyang at night this week and last and that the intrusion demanded retaliatory action, the state news agency KCNA reported on Friday.
"The ROK (South Korea) should immediately stop such irresponsible and dangerous provocation that may cause an armed conflict and lead to a war between the two sides," the ministry was quoted as saying.
In its statement, South Korea's Joint Chiefs of Staff said it "cannot confirm the truth of North Korea's claims", adding: "All responsibility for the recent series of events" lies with Pyongyang.
It cited "despicable, low-grade and internationally embarrassing acts of filth and garbage balloons and other provocations."
More balloons were being sent on Friday, it said.
North Korea has been floating thousands of balloons with trash attached into the South since May, exacerbating tensions between the two countries.
Pyongyang says they are a response to some activists and North Korean defectors in South Korea who fly balloons into the North carrying aid parcels and leaflets criticising leader Kim Jong Un.
KCNA distributed photos, including ones showing a blurry, triangular object labelled as a "drone" dropping another object labelled as "bundle of leaflets". One image also showed a cloud of small objects that was labelled as "scattered leaflets."
Another photo showed black, yellow and white leaflets comparing the economic situation in the South to the impoverished North and criticising North Korean leader Kim Jong Un by name.
South Korea's Yonhap news agency cited an official at the Joint Chiefs of Staff as saying it needs to look into whether a private group had sent leaflets into the North.
In December five North Korean drones crossed into South Korea, prompting Seoul to scramble fighter jets and attack helicopters, and try to shoot them down, in the first such intrusion since 2017.
The two Koreas are still technically at war after their 1950-53 war ended in an armistice, not a peace treaty, and the North has long denounced defectors as "human scum".
There will be no more warnings and the North will immediately take action in the event of another drone being sent by the South into its territory, North Korea's foreign ministry said.
