The East By West ferry was travelling towards Days Bay, Eastbourne from Queens Wharf and left just after 6am on Friday.
The man was the only passenger onboard, and was no longer on board when the vessel reached the dock.
Detective Senior Sergeant Rachel Boyd said police would not be releasing any details of his identity at this stage.
He is yet to be found, but a potential location of interest had been identified in the Wellington Harbour.
"Following the report of a man falling overboard Maritime New Zealand Rescue Coordination Centre NZ coordinated a thorough on-water search effort using detailed modelling and analysis of the harbour and search efforts," Boyd said.
"The search involved up to 14 vessels and a rescue helicopter at its peak."
The search continues on Monday coordinated by the police maritime unit with help from the navy.
Boyd said police will continue to update the man's family as the search for him progresses and are providing them with support.
