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.