The National Forensic Service conducted tests and confirmed them as animal bone fragments, the maritime ministry said. The Sewol sank off Jindo island on 16 April 2014, killing 304 people, almost all of them children.
The bodies of nine people were never found. Relatives have campaigned hard for them to be recovered. The ship was raised last week after almost three years on the sea floor and put onto a platform to be towed to port.
Early on Tuesday, South Korean officials said bones had come out of a window of a passenger room during work to drain the ship.
At a press conference, Lee Cheol-jo of the Ministry of Oceans and Fisheries said tests were needed to determine whether they came from one or more individuals.
But in a subsequent late-night statement, the ministry said the bones were not human.