The city government of the capital Seoul has asked prosecutors to charge Lee Man-hee, the founder of the Shincheonji Church, and 11 others.
They are accused of hiding the names of some members as officials tried to track patients before the virus spread.
South Korea is battling the worst coronavirus outbreak outside China.
The country has reported 3,730 cases and 21 deaths so far. More than half of all infections involve members of the Shincheonji Church of Jesus, a fringe Christian group.
Authorities say Shincheonji members infected one another in the southern city of Daegu last month, before fanning out around the country.
One senior member, Kim Shin-chang, told the BBC’s Laura Bicker that the church was “very sorry for causing concern”.
He admitted that some church members had been afraid to reveal their identities but said the church had now revealed all of its information, including all its locations and members.
“We were worried about releasing this kind of information because of the safety of our members, but we believe right now the most important thing is to fully cooperate with the government,” he said.
On Sunday the Seoul City government filed a legal complaint to prosecutors against 12 leaders of the sect. They are accused of homicide, causing harm and violating the Infectious Disease and Control Act.
All 230,000 members of the church have been interviewed. Nearly 9,000 said they were showing symptoms of coronavirus.
The sect’s leader, Lee Man-hee, claims he is the Messiah. He has also been tested for the virus and is awaiting the results.
Roman Catholic churches remain closed, major Protestant groups have cancelled Sunday services and all Buddhist events have been called off.