The East By West ferry was travelling towards Days Bay, Eastbourne from Queens Wharf and left just after 6am.
The man was the only passenger onboard, and was no longer on board when the vessel reached the dock.
The man is described as in his 40's, fair skinned, around 180cm tall with dark hair. He was wearing a dark jacket with a zip and dark pants.
Maritime New Zealand Rescue Coordination Centre NZ coordinated a on-water search effort on Friday using detailed modelling and analysis of the harbour. It involved up to 14 vessels at its peak.
A helicopter, the police maritime unit and the coastguard including volunteers, as well as other vessels, took part in today's search.
The man had not been located and active searching had been temporarily suspended pending a review, Senior Sergeant Rachael Boyd said in a statement.
Anyone who had a family member or friend who matched this description and who had not returned home as expected should contact the police, she said.
Anyone with information that may assist in identifying this person, should call the police on 105, referencing file number 240524/6000.
East By West ferries to resume operation on Saturday
East by West ferries, Greater Wellington regional council and Metlink have thanked all those involved in today's search.
In a statement issued on Friday evening, East By West ferries general manager Mat Jonsson said the ferry crew issued a mayday call as soon as they became aware a passenger was missing.
A second harbour ferry was called in to assist with the search and other vessels also responded to the mayday call, he said.
"Conditions on the harbour this morning were very still. The main cabin of the vessel involved is fully enclosed, and the top deck has barriers around the passenger area to stop someone accidentally falling overboard."
East By West ferries has not been operating today but will resume normal services on Saturday.
Greater Wellington chair Daran Ponter said the regional council's thoughts were with the missing passenger, their loved ones and staff who were on the East By West ferry this morning.
"We also wish to extend our appreciation to maritime police and all the crews who responded to this emergency and are helping with the search," he said in a statement.
It was likely that a rahui that would restrict the gathering of kai moana and recreational activities would be placed on part of Wellington Harbour and people should comply with it, he said.
Metlink group manager Samantha Gain described the ferry company's response to the emergency as "exemplary".
"Under extremely difficult circumstances, East by West followed emergency procedures and committed all available resources to the search. Affected crew are receiving support and Metlink stands ready to give our ferry operator any assistance it requires," Gain said in a statement.
Deputy harbour master Patrick Atwood said the search and rescue operation was well coordinated and "the number of crews that joined the search was impressive".
RNZ
