The search resumed this morning using the police Eagle helicopter, a Coastguard plane and Coastguard vessels from Whitianga and Great Barrier Island.
At 2pm a private vessel came across the missing boat named Tubby, approximately 24 nautical miles off the coast of Whitianga.
No one was on board and the boat is in the process of being recovered.
The boat, named Tubby, was described as a white 6-metre long "Mac" centre console plastic boat with no top.
The search operation for the man, in his 50s, continues this afternoon, involving a Coastguard fixed-wing plane and Coastguard vessels from Whitianga and Great Barrier Island.
Anyone who can provide information about sightings of the boat from 9am on Friday, or who finds any items of interest that may be related, is asked to contact 111 and quote event file number P04906827.