"I would like to offer my sincere apology to the people on behalf of the members," said Shincheonji head Lee Man-hee, his voice breaking.
The 88-year-old twice got down on his knees to bow before reporters in Gapyeong, his head to the floor.
"Although it was not intentional, many people have been infected," he said.
"We put our utmost efforts but were unable to prevent it all. I seek the forgiveness of the people.
"I am very thankful to the government for its efforts. I also seek the forgiveness of the government."
Lee is revered by his followers as the "Promised Pastor" who will take 144,000 people with him to heaven on the Day of Judgement, and his group is often condemned as a cult.
A 61-year-old female member developed a fever on February 10 but attended at least four church services in Daegu - the country's fourth-largest city with a population of 2.5 million and the centre of the outbreak - before being diagnosed.
South Korea's case numbers are expected to rise further as authorities carry out checks on more than 260,000 people associated Shincheonji.
Seoul's city government has asked prosecutors to press charges, including murder, against him and 11 other sect leaders for failing to cooperate in containing the spread of the deadly coronavirus.
Lee insisted that the group was "actively cooperating with the government".
"We will do our best and not spare human and material support," he added, pausing occasionally to wipe tears from his eyes as protesters shouted abuse.
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