The 43-year-old and his wife were arrested Sunday for homicide after the couple's relative found the decomposed bodies of the children at their home next to the pastor's church in Boseong county near the southwest coast.
Forensic examination showed the 10-year-old girl and the two boys aged five and eight had no food in their stomachs and had suffered severe bruising all over their bodies, the Jeonnam Provincial Police Agency spokesman told AFP.
The couple told police they had tried to cure their children, who were suffering from colds and high fever, with fasting and prayer and by repeatedly whipping them to "drive bad spirits away".
"We believe the children had not been fed since January 23 before they eventually died on February 1 or 2," the police spokesman said.
The couple allegedly whipped each child 39 times with a belt or a fly swatter on five separate occasions, citing a Biblical verse.
Police said they cited Proverbs 23:13-14, which reads: "Do not withhold discipline from a child; if you punish them with the rod, they will not die. Punish them with the rod and save them from death."
Their fourth child, a year-old baby, was taken into protective custody by police and was in good health.