Archaeologists so far have uncovered a 35-foot section of one side of the ship, the Italian news agency ANSA reported. The ship was discovered during a rescue dig at the site of a new road.
Ostia was located at what was then the mouth of the Tiber River. The Emperor Claudius built facilities there that turned the town into a major port.
Anna Maria Moretti, archaeological superintendent for Rome and Ostia, said restoring the ship "will be an extremely delicate operation."
"We're keeping it constantly covered in water so that the wood doesn't dry out," she said. "The wreck must be treated with highly sophisticated preservation techniques."
Culture Minister Giancarlo Galan told ANSA viewing the ship "gives you goose bumps." He said the find and its location have also added to archaeologists' knowledge of the ancient shoreline.
Ostia Antica, the Roman-era port, is second only to Pompeii in showing what a Roman Empire town looked like.
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