Divers were attempting to retrieve the body trapped underwater in debris left when a vessel bound for the Sicilian city of Messina struck the Genoa control tower, the Italian news agency ANSA reported.
Officials said about 14 people were in the tower at the time of the accident, which sent the structure tumbling into the waters.
The accident occurred during a shift change, so more people were in the tower than usual, ANSA said.
Four people were rescued and hospitalized, two in serious condition.
Investigators said the container ship, the 40,500-ton, 655-foot Jolly Nero flying the Italian flag, was impounded and an investigation into manslaughter charges has been opened.