Yoo Byung-un is wanted on charges of embezzlement,negligence and tax evasion related to an alleged web of business holdingscentered around an investment vehicleowned by his sons that ran the shipping company Chonghaejin Marine.
Chonghaejin operated the Sewol which capsized in Aprilkilling more than 300 people.
Yoo, who is reported to be 72, is said to have been aco-founder of the Evangelical Baptist Church that runs the Anseong compoundsouth of Seoul.
Prosecutors say they did not expect to find Yoo or hiseldest son at the commune but were looking for evidence. Arrest warrants have been issued for his twosons, the younger of which is believed to be in the US.
"This investigation is about personal wrongdoings onthe part of Yoo Byung-un and sons related to the management of ChonghaejinMarine," Kim Hoe-jong, a senior prosecutor told the Reuters news agency.
About 1,200 police officers were on standby and helicoptershovered overhead as dozens of investigators entered the compound which has afreshwater fish farm and produces organic food. Followers had earlier preventedthe authorities from entering - accusing the government of religiouspersecution.
Prosecutors last month raided a house in Seoul believed tobe Yoo's plus other locations where he was thought to be evading summons toappear for questioning.
The Sewol ferry capsized on April 16 during a journey fromthe mainland port of Incheon to the holiday island of Jeju. Most of the victimswere children on a field trip from a high school.
Yoo’s allies have claimed he is not involved in the ferrycompany, and that in the last few years he has been working as a photographer afteradopting the name Ahae.
Michael Ham, managing director of Ahae Press, said Yoo hasspent “every single day of the past four to five years focusing on hisphotography work," and was not directing any firm tied to the sunkenferry.
"I am dismayed at the media reports linking him to theSewol incident and suggesting that he is directly responsible for thistragedy," Ham said. "These claims cannot be further from thetruth."
The captain and three officers from thesunken Korean ferry Sewol have been charged with manslaughter.
Prosecutors claim the ferry was overloaded with cargo andinstable after its capacity was expanded in 2012.
The elder Yoo was jailed for fraud in the 1990s but wascleared of complicity in the suicides of 32 workers of a company linked to hischurch in 1987.