The Ministry of Oceans and Fisheries had earlier said salvage crews found bones measuring 4 to 18 centimeters (1.5 to 7 inches) that were likely to be the remains of one or more of the nine missing passengers.
But after inspecting the bones, investigators from the National Forensic Service concluded that they were from unidentified animals, not humans.
The discovery of the presumed human bones had triggered an angry reaction from the missing victims' relatives, who criticized the government's salvage operation as poorly planned and questioned whether other remains might have gotten lost while workers raised the sunken ship last week.
Workers have just completed a massive operation to lift the corroding 6,800-ton Sewol from the sea, and recovering the remains of the missing victims would put the country a step closer to finding closure to one its deadliest maritime disasters.
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The bones were found near a beam beneath the front side of the ferry, which had been loaded onto a heavy lift transport vessel that will carry it to port.
A total of 304 people died in the disaster. Rescue workers recovered the bodies of 295 people - most of them students on a high school trip - before the government ended underwater searches in November 2014, seven months after the ship sank.
Relatives had expressed concern that remains of the missing victims could slip out through the holes and get lost.
Earlier today, relatives of the missing passengers participated in an emotional memorial service on a boat near the transport vessel, with representatives of Catholic and Protestant churches and Buddhists delivering prayers wishing for the remains of the nine to be recovered.
Relatives threw into the sea yellow roses, a color that has become the symbol of their suffering, and watched from afar as crews on the transport vessel continued to empty the ferry of water and fuel.
Once the ferry reaches the port in Mokpo, investigators will spend about a month cleaning it and evaluating it for safety.
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