Police are searching for two men who they believe were talking to another man before he was reported seen in the water near Auckand's waterfront ferry terminal.
The police dive squad has arrived in Auckland and are to search the water later this afternoon.
The man was sighted at 4.35am today and police have been searching the area since.
Police say they are using an official police launch, as well as the Eagle helicopter to assist in the search.
The man is yet to be identified and police say they are "very concerned" for his safety.
Police have spoken with witnesses and are reviewing CCTV footage in hopes to understand the circumstances of why the man was in the water and the events leading up to the incident.
"We are still working to establish the circumstances surrounding the incident. Initial inquiries report that the man was talking to two men before he was seen in the water," said detective senior sergeant John De Heer.
Ferry operations departing from the Downtown Ferry Terminal have been changed until further notice and people are advised to expect delays.
Auckland Transport says services to Half Moon Bay were suspended after 2.30pm and buses will be operating as a replacement service from Queens Wharf.
Police are asking anyone else who has information that may assist police to contact Auckland City crime squad on 09 302 6557.