Police say the body was found Monday evening by the dive team with help from the Navy.
Formal identification had not yet taken place.
The missing Wellington man was the only passenger on board the East By West ferry, which traveled from Queens Wharf towards Days Bay, Eastbourne, just after 6am on Friday.
He was no longer on the ship when it reached the dock, prompting a massive, multi-day search involving more than a dozen boats and helicopters.
Police identified the missing man Monday but released no details.
Local iwi Te Āti Awa has now placed a rāhui over the inner harbor until 6am on Thursday.
“The iwi are requesting that Kaimoana not be removed from the Inner Harbor out of respect for the whānau pani (grieving family) as they face the challenge ahead,” police said.
Police said they were still investigating.
Wellington harbor master Grant Nalder told RNZ that such an incident had happened in the past, but it was “rare”.