A daughter of the victim was injured in the crash, which occurred when the out-of-control boat struck the gondola as it shoved off from a dock near the city's Rialto, Agenzia Giornalistica Italia reported.
The entire family of five was knocked into the canal by the force of the crash. It was believed the father was crushed between the two vessels, said a translated report from Italy's La Repubblica.
Investigators said it appeared the motor boat skipper made a sharp evasive maneuver to avoid an oncoming vessel but lost control of the boat and hit the gondola. The Rialto area of the Grand Canal is notorious for heavy boat traffic.
The gondolier apparently saw the oncoming boat and tried to hustle the passengers back to the dock but did not have enough time, La Repubblica said.