The man had not been seen since late Tuesday afternoon when the small vessel he was on sank.
A survivor of the upturned boat raised the alarm after a treacherous swim to shore in large swells.
Police were called to the harbour at 5.50pm on Tuesday. A spokeswoman confirmed one person had been found safe and did not need medical attention.
The boat was towed back to shore on Tuesday evening but, despite ongoing efforts, the man remained unaccounted for that night.
On Thursday, the Police National Dive Squad had been called in to help search.
This morning the missing man’s family gathered harbourside, sitting at the edge of the boat ramp near Māngere Bridge.
The family told the Herald they have been coming to the bridge for the past few days since the man was lost overboard.
Iwi have been advised and a rāhui has been put in place covering much of the area for at least seven days.
On social media, Auckland Manurewa-Papakura ward councillor Daniel Newman expressed his gratitude to the Papakura Coastguard volunteers who searched.
The Papakura crew had joined Titirangi Coastguard, Auckland Airport hovercraft and the Westpac Rescue Waikato helicopter.
“I am profoundly sorry to the family of the missing person. I thank our first responders for their efforts, our community thanks you all.”
The search had been concentrated near Auckland Airport but went as far as the Manukau Heads and the eastern bays such as Laingholm.