Authorities had earlier announced the pieces were human -- raising the prospect of closure for families of at least some of the nine passengers whose bodies were never found after the 2014 maritime disaster.
But the ministry corrected its initial statement, declaring: "According to test results by the National Forensic Service, they have been confirmed to be seven animal bone fragments."
They were suspected to be pig bones, South Korea's Yonhap news agency said, citing forensic officials.
The wreck was brought to the surface last week in a complex salvage operation, nearly three years after it went down with the death of more than 300 people, and placed onto a semi-submersible ship that will finally bring it to shore.
Almost all the victims were schoolchildren.
Divers wrapped up their search in November 2014. But the failure to account for nine bodies raised the prospect they could still be inside the vessel and left their families emotionally trapped in the grieving process.
In an urgent briefing, the ministry had said salvage workers had recovered six bone fragments believed to be from victims missing since the disaster. The fragments were found on the deck of the semi-submersible carrying the Sewol.
"They are suspected to have been found among sand that leaked out from an opening at the entrance of the vessel or through a window," said Lee Cheol-Jo, a senior ministry official in charge of the salvage operation.
The operation to raise the 145-metre ferry, which has cost more than $82 million, is believed to be among the largest-ever recoveries of a wreck in one piece.
The salvage operation had been a key demand of the families of the nine missing victims, including four schoolchildren and two teachers.
After the divers ended their search, a handful of relatives set up home at Paengmok, a port an hour away from the accident site.
The semi-submersible is expected to set off on Thursday for Mokpo, a large port on the southern coast some 87 kilometres (54 miles) away.
As part of the operation, underwater barriers were set up around the wreck and searches will be carried out in the area as well as on board the Sewol.
The sinking, one of the country's worst-ever maritime disasters, dealt a crushing blow to now-ousted president Park Geun-Hye.
Investigations concluded the tragedy was largely man-made -- the cumulative result of an illegal redesign of the ship which made it top-heavy, an overloaded cargo bay, inexperienced crew and a questionable relationship between the ship operators and state regulators.
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