South Korea tracked the drones crossing from North Korea over what is known as the Military Demarcation Line between the two countries, Yonhap reported.
South Korea's transport ministry said earlier flights departing from its Incheon and Gimpo airports were suspended following a request from the military.
The suspension began at 1:08 p.m. (0408 GMT) at Gimpo and at 1:22 p.m. at Incheon and lasted for about an hour before flight departures resumed at around 2:10 p.m., a ministry official told Reuters.
The official did not provide further details on the suspension.