The Pākehā man in his 40s was the sole passenger on the first East by West Ferry crossing from Queens Wharf to Days Bay early on Friday morning, but was not on board when the ferry arrived at its destination.
The search was being led by the Police Maritime Unit with help from the Navy.
On Friday, the harbour was searched by police, coastguard and other vessels.
On Saturday, police said they were no longer searching the water and were concentrating on the coastline.
They have appealed for information about the missing man or anyone missing who matches the description.
He is described as fair-skinned, about 180cm tall with darker hair and believed to be aged in his 40s. He was wearing a dark jacket with a zip and dark pants.
Police said they would release further information when they were in a position to do so.
