The trio flew the aircraft between September 2025 and January, Chung said, citing an ongoing investigation by police and the military.
Drones crashed on two occasions in North Korea, in line with claims made by Pyongyang, Unification Minister Chung Dong-young said.
On two other attempts the drones returned to Paju, a border settlement in South Korea, after flying over Kaesong, a city in North Korea, Chung said.
South Korean authorities were investigating the three civilians on suspicion of violating the aviation safety act and breaching criminal law by benefiting the enemy, he said.
Some officials at South Korea's military intelligence agency and the National Intelligence Service were also under investigation for alleged involvement with the trio, he said.
"We express official regret to the North," Chung said, adding that the government was taking the drone incursion incidents very seriously.
North Korea has reacted angrily, saying last month that drones from South Korea entered its airspace, after another intrusion in September.
Kim Yo-jong, the powerful sister of North Korean leader Kim Jong-un, urged Seoul to investigate the incident, warning provocations could result in "terrible situations".
Chung also expressed regret over South Korea sending 18 drones to North Korea under the direction of ousted president Yoon Suk-yeol.
"It was an extremely dangerous incident aimed to induce an attack against South Korea by sending 18 drones on 11 occasions, to sensitive areas in North Korea including the airspace over the Workers' Party office," he said.
South Korean prosecutors have indicted Yoon, who was ousted in April 2025, on charges that include aiding an enemy state.
They accused him and his military commanders of ordering a covert drone operation into the North to raise tensions and justify his martial law decree.
Yoon denies wrongdoing.
17°C