Hall said the operation was launched after the vessel was reported missing at 3.30pm. Eleven people were onboard.
"A shoreline search around South Head and Te Oneone Rangatira Beach will continue for a few more hours," Hall said.
"The air search has now ceased and is scheduled to recommence tomorrow morning from 7am, weather permitting.
"Conditions are not suitable for an air search to continue tonight due to a significant sea swell. Visibility is poor, which would put rescue aircraft and their crews at risk."
Hall said inquiries were being made into what caused the maritime tragedy and how those onboard ended up in the water.
He didn't have any details on those involved in the tragedy, including their ages, genders or how, or if, they knew each other.
"Part of the investigation is determining who was on board."
Police had been told there were life jackets on board, but did not yet know if they were being worn.
He did not know how many of those on board were crew members.
Two rescue helicopters were at the scene "promptly", Hall said, allowing them to "pluck (the rescued) from the water".
Asked if there were other vessels in the area at the time if the capsize, Hall said that was part of the investigation.
"It shouldn't have been out there"
The former skipper of the Francie has tonight described it as an "excellent little boat", but said it should not have been on the harbour today.
"It shouldn't have been out there. It was too rough ... it's a terrible thing," Rod Bridge said.
He also runs a charter business, which he declined to name, but said he had disappointed his customers by calling off today's outing because of the conditions.
"I stayed home, I'm not stupid .. the wind was coming up and the swell was coming up. You wouldn't go out over the bar."
One customer had called him this evening, after hearing of the tragedy involving the Francie.
Bridge owned the Francie, which is made of steel, for two or three years. He bought it about four or five years ago, when it was around eight years old.
"It was a flaming good little boat. That's why I bought it."
He believed the boat's owner, Bill McNatty, was the only skipper of the Francie.
Charter owner: Sad to miss one of our fellow skippers
The owner of a charter fishing company that also takes groups out on the Kaipara Harbour said it was a sad situation for all.
The man, who asked not to be identified, said he knew the skipper of the Francie and was just waiting to see whether or not he was one of those who had died in the accident.
Wayne Bollond was having a drink at Helensville's grand Hotel as he anxiously awaited news of his old mate Bill McNatty and the others on board the Francie.
Wayne worked for McNatty for about 18 months and said he was an extremely experienced skipper who'd made that same trip countless times.
He said the Francie was a purpose-built steel charter boat that would have been fine in marginal conditions.
A typical trip would involve catching a few kahawai at Potu Bank and then going for snapper at the 'Graveyard' - a mussel bed on the inside of the bar at North Kaipara head.
"It's a very, very safe boat - I have total respect for it. I believe something else would have happened and that's when people lose their lives. That's how safe you've got to be out there and that's how safe we are. We're professionals."
He said there was a "confused sea" over the bar that required skippers to notify Coastguard prior to entering it and upon leaving it.
A spokesman for Maritime NZ said it was not appropriate for the organisation to comment about the situation, given the police response and investigation was still underway.
However, he encouraged anyone who may have information they would like to provide to authorities to make contact.
"If people have maritime information they believe is important or have concerns they wish to raise, then please contact Maritime NZ.
"We will be grateful for their call.''
Police to boaties: "steer clear"
Police have also appealed for boaties and pilots of aircraft not involved in the search to "steer clear" of the area.
"Emergency services require a safe working space around South Head," police said.
An online booking service for Francie states: "Enjoy a day's fishing for any of the predominant Kaipara fish species - kahawai, snapper and gurnard and in season trevally, maumau and kingfish".
Daily boat hire costs from $700-$800.
In 2012 the boat was involved in the rescue of a ketch cast adrift after its sails blew out and it had engine problems.
A story in the Kaipara Lifestyler quoted then Francie skipper Bridge as saying: "Another half an hour and that would have been it - they would have foundered in heavy seas on the bar."
A rescue chopper and Coastguard were also involved in the 2012 water rescue.
Earlier, a spokeswoman for the Auckland Westpac Rescue Helicopter said they had been called to an accident that left "multiple people in the water".
Lifeguards said 11 people were in the water after a boat flipped over.
The Muriwai Surf Lifesaving Club was being used as a base for the emergency operation.
The Transport Accident Investigation Commission confirmed it had opened an investigation into what it described as a "marine accident".
"It is tracking the continuing search and rescue operation, and deploying two investigators to the scene who are expected to arrive in the morning," it said.
"The Commission's inquiry will seek to explain the circumstances and causes of the accident, with a view to helping prevent similar accidents in the future. The Commission is unable to confirm further details of this afternoon's events while the search and rescue operation continues."
MetService said the mean wind speed in the area, recorded at 5pm, was 28km/h gusting 50km/h.
Meteorologist Tom Adams said that at 6pm, that had changed to 31km/h and gusting 48km/h.
The air temperature in the area is 18 to 19C and a few light showers are expected.
The Kaipara Harbour features one of the toughest bar crossings in New Zealand for boaties to encounter.
"They are common around the country in areas such as harbours and rivers," an education page on Coastguard Northern Region's Facebook page says.
"If you go boating and want to get out into open seas you usually have to navigate them and they can also be extremely dangerous. They are called Bars, such as can be found at Manukau, Kaipara, Raglan and many other areas in New Zealand and around the world.
"Many experienced boaties have got into difficulty crossing a bar and each year, boats are damaged and people are killed or injured when attempts to navigate bar crossings go wrong."
Kaipara Harbour's bar has resulted in as many as 110 shipwrecks.
• Anyone who has concerns about the welfare of relatives in relation to this incident is asked to attend Helensville Police Station or to call 111 for assistance.