SIX people were killed and three are missing after a container ship crashed into a control tower in the northern Italian port of Genoa.

The tower, which was more than 50 metres high, collapsed into the water late on Tuesday after being struck by the prow of the vessel, the Jolly Nero.

Two of the dead were coastguard officers and a third was a pilot for the port, the coastguard said.

The three other victims have yet to be identified. Two were recovered from the wreckage of the tower's lift, a firefighters' spokesman said.

The accident happened as staff were changing shifts and there were 13 people in the tower when it was struck, the coastguard said.

As well as the dead and missing, officials said four people were injured and had been taken to hospital. Two were seriously hurt and one had lost a foot. The crash occurred in calm conditions as the Jolly Nero was manoeuvring out of the port.

Genoa prosecutor Michele Di Lecce has opened an investigation and is focusing on a possible malfunction of the ship's engine or steering mechanism.

The crash is the most serious maritime accident in Italy since the Costa Concordia luxury cruise liner struck a rock and capsized off the island of Giglio in January 2012, killing 32 people.

"There's no logical explanation because two tug boats were moving the ship and there was a port pilot on board and sea conditions were optimal," the head of the Genoa Port Authority, Luigi Merlo, said.