Police say the body was found by the diving squad with help from the navy on Monday night.
Formal identification had not yet been carried out.
The missing Wellington man was the only passenger aboard the East By West ferry, travelling towards Days Bay, Eastbourne from Queens Wharf just after 6am on Friday.
He was no longer on the vessel when it reached the dock, prompting a search a large-scale, multi-day search by more than a dozen boats and helicopters.
Police identified the missing man on Monday but did not release any details.
A rāhui has now been placed over the inner harbour by local iwi Te Āti Awa until 6am Thursday.
"The iwi request that kaimoana is not taken from the inner harbour out of respect for the whānau pani (grieving family) as they face the challenge ahead of them," police said.
Police said they were still investigating.
Wellington Harbourmaster Grant Nalder told RNZ such an incident had happened in the past but it was "infrequent".
