Yoo, the target of the country's largest manhunt, was found dead in an orchard on June 12. Police identified his body this week.
"We are aware there are many questions and did our best, but it was impossible to determine the cause of death," an agency official, Lee Han-young, told the news conference.
The autopsy found no evidence of trauma from a weapon or strangulation, although there was heavy decomposition damage to the tissues in the head and neck, Lee added.
Yoo headed the family that owned the operator of the ferry, Sewol, which capsized and sank on April 16 on a routine journey, killing more than 300 people, many of whom were children from the same school on a class trip.