Live television reports showed police officers, many in full riot gear, streaming into the sprawling church and farming complex at around 8:00 am (0000 GMT) in Anseong, 80 kilometres (50 miles) south of Seoul.
A spokesman for the Gyeonggi province police force said 6,000 officers were involved in the raid.
The huge operation came a day after President Park Geun-Hye urged police and prosecutors to step up a manhunt for Yoo Byung-Eun, 72, a leading member of the Evangelical Baptist Church of Korea.
"Yoo must be brought to justice," Park told a cabinet meeting.
He is wanted for questioning on possible charges of embezzlement and criminal negligence, as prosecutors investigate the extent to which the Sewol disaster was caused by a lack of safety standards and regulatory violations.
Yonhap news agency said the raid had netted three church followers suspected of helping Yoo evade a nationwide dragnet put in place after he defied an official summons to surrender to prosecutors last month.
Yoo has no direct stake in Chonghaejin, but his children and close aides control it through a complex web of holding companies.
A reward of 500 million won (USD 490,000) has been offered for information leading to the capture of Yoo and 100 million won for that of his eldest son, Yoo Dae-Kyun.
Police had raided the church complex in Anseong three weeks ago but came away empty-handed, amid reports that Yoo may have fled overseas.
The church followers erected a barricade at the entrance to the complex, but made no move to block the police today after they forced their way through.
