The 50-year-old man, whose identity has not been released, worked for Bidfreight Port Operations, a local stevedore company, and was loading the CSCO vessel called Shan Hai.
The ship, which was launched in 1998, was scheduled to leave port this week, but will berth at Durban Point while investigations take place.
A full enquiry has been launched with the South African Maritime Safety Authority expected to play a lead role.
The police have suggested that structural damage to the crane may be to blame. With investigations at an early stage, the cause of the accident is not yet clear.
An eyewitness told Cranes Today: “The jib fell across the deck with the end protruding over the side, then it buckled with the force and parts of it snapped off.”
He continued: “The cab was on the main frame above the gearing, which was where the crane snapped. The operator was crushed when the whole mechanism crashed onto the deck.”