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.
The sinking of the Sewol shocked the nation. Most of those on board were teenagers from the same high school. Many obeyed erroneous crew instructions to remain in their cabins as the ship sank.
The nine victims who have yet to be recovered are four school children, two teachers and a married couple and their child.
The ship is expected to reach Mokpo port later this week, where it will be met by families of the victims, before being cleaned and searched for their remains.
On Tuesday morning relatives of the nine held a memorial service on a boat near the raised vessel.
"The ship has come up, but not the nine people inside it,'' Lee Geum-hee, the mother of a missing school girl, told local media.
"Please don't forget there are people inside the dirty, rusty and smelly wreckage... Please do the best and let us bring them back home.''
The disaster was blamed on a combination of illegal redesigns, cargo overloading, the inexperience of the crew member steering the vessel, and lax government regulations.
The ship's captain was later convicted of murder.
Remains found on the raised Sewol ferry that were thought to come from one of the disaster's missing victims are from animals, South Korean officials say.