"I would like to say that I am sorry to the citizens about the result of the operation conducted in response to the North's drone provocation," Lee was quoted by Korean news agency as saying during a session of the parliament's national defense committee.
The minister also refuted media reports that the drones flew all the way to Yongsan, Seoul's central district, where the office of President Yoon Suk Yeol is located.
On Monday, Korean media reported, citing South Korean military, that a number of drones believed to be North Korean had crossed the inter-Korean border. South Korea tried to shoot the drones down and scrambled fighter jets and attack helicopters to intercept them. One of the aircraft, a KA-1 light attack plane, reportedly crashed during takeoff.
Four small North Korean drones flew in the area of Ganghwado Island in South Korea, and another flew up to the northern region of the metropolitan area, including Seoul. Yonhap later said that one drone managed to return back to the North, while the remaining four disappeared from radars.
The South Korean Defense Ministry called the violation of its airspace by North Korean drones "a clear provocation" and pledged to respond decisively.