Prosecutors in Incheon said Yang Hoe-jung turned himself in at their office, which is investigating the role of businessman Yoo Byung-un in the sinking of the ferry Sewol.
Mr Yoo's body was found by a farmer in an orchard on June 12.
The structurally defective and heavily overloaded ferry capsized and sank on a routine journey on April 16, killing 304 people, 250 of them teenagers from the same school on a class field trip. Twelve of their teachers also died in the incident, the country's worst maritime disaster in 44 years.
The driver was the last among a group of people close to Mr Yoo who had been wanted for allegedly helping him elude South Korea's biggest manhunt.