Ranger said the dive squad's primary focus would centre on an area of about six nautical miles between the Bowentown Bar and where the boat was found.
That was about three-quarters of a nautical mile north of the Bowentown Bar, he said.
Ranger said shoreline searches of Waihi Beach around the northern rocks and the Bowentown entrance were also due to be undertaken yesterday during low tide.
A member of the Waihi Beach Surf Club confirmed club members would be involved in the shoreline search.
Sonar searches of the seabed were undertaken during yesterday's search by naval officers.
Chief Petty Officer Daniel Bramley, from the Auckland-based HMNZS Matataua unit, said Navy personnel spent about six hours yesterday sonar mapping the seabed in the key search area looking for any objects of interest.
Bramley said he was yet to analysis the sonar data.
Ranger said there were no reported sightings of the missing man and his name was unlikely to be released at this stage.
A small group of people, believed to be family or friends of the missing man, also searched the rocks at the base of the Bowentown headland on Wednesday.
They declined to comment.
Eddie Evans, who has lived in Waihi for 17 years, and knows the area well, said he was saddened to hear about the fisherman's disappearance.
"The bar is treacherous, particularly in choppy conditions, especially if you're unfamiliar with it.
"Unfortunately, this is not the first time someone has tipped out of their boat while crossing the bar and probably won't be the last," he said.
