Around 14 people were in the 50-metre high glass-topped tower when it was hit by the ship's stern as it ploughed into the dock. Some were thrown into the cold water, while others were trapped under rubble or in a lift which may have toppled into the sea, media reports said.
The vast red ship was following protocol and navigating towards the control tower, when it failed to reverse properly before turning out into open sea and rammed into the concrete and metal structure. Initial reports suggested it had suffered a mechanical failure.
"It was a manoeuvre done hundreds of times. We're all wondering what could have happened," he said.
One of the victims was reported to be Daniele Fratantonio, 30, who worked for the coast guard operations centre, while another was said to be a 47-year-old father of two.
More From This Section
Rescue workers dived into the inky waters around the port -- the busiest in Italy -- in a frantic search to find those missing after the crash, which seriously wounded four.
One of the pilots was quoted as saying: "Two engines seem to have failed and we lost control of the ship."
Rescue workers were also using dogs trained to find people in earthquake zones to see if survivors were trapped under the rubble.
At dawn, a mobile telephone which began to ring beneath the wrecked structure raised the hopes of locating survivors, but it rang off before rescue workers could localise the sound.
The accident happened during a shift change at the vast metal tower, which bent over by 45 degrees before collapsing, leaving only what looked like an emergency staircase standing.
"I heard a terrible din and rushed out of my cabin," Roberto, the port's night watch, told La Repubblica newspaper. "It was an incredible sight: the control tower was leaning perilously.