The discovery comes a week after the vessel was raised upright in a major salvage operation.
32 of the 4,229 people on board died, when the ship capsized after crashing against rocks.
Two people remain missing and presumed dead: Russel Rebello of India and Maria Grazia Trecarichi of Sicily.
Italy’s protection agency says divers will try to recover the remains, which were spotted in the sea near the central part of the ship, where survivors say the two were last seen.
Authorities say DNA tests will determine the identity of the remains. Officials say relatives of the two victims have been notified.
The captain of the ship, Francesco Schettino is accused of manslaughter, causing the shipwreck and abandoning ship.
The ship is due to be towed away sometime next year, and eventually broken up from scrap.