More than 4,000 South Korean police officers raided a branch of the Evangelical Baptist Church in Anseong on Wednesday.
They were searching for people thought to be linked to the Sewol ferry disaster, particularly those believed to have assisted businessman Yoo Byung-un, who is said to be the owner of the sunken vessel.
Yoo is a co-founder of the church running the Anseong compound.
He remains at large, but three church members were detained on suspicion of aiding his escape and one for interrupting the search.
Hundreds of worshipers sat outside the commune to protest the raid.
Yoo Byung-un allegedly controls the Sewol ferry’s operator through a complex web of holding companies linked to his children and close associates.
The raid followed the start of the trial of 15 surviving crew members.
More than 300 people were declared dead or missing after the ferry sank in April, sparking a police manhunt for Yoo and his sons. They have so far evaded arrest.