A boy and a girl are in critical condition after the 2.37pm incident. They were airlifted to Starship Hospital in Auckland.
A man in his 60s has been flown to Waikato Hospital in a serious condition.
The man was resuscitated at the scene twice with the assistance of surf life-savers and St John.
A woman in her 30s was also among those caught up in the incident, suffering minor injuries. It was thought there were five people on the boat, and police said all had been accounted for.
Multiple ambulances and rescue helicopters were sent to help soon after 2.30pm.
A witness said three rescue helicopters had landed in the area, a popular Coromandel holiday spot, and the Coastguard was also involved.
"Coastguard boat still out in water towing boat upside down - it had turned over but when they got person out it flipped again and went back out to sea."
Video shot at the scene showed people holding up a sheet as ambulance officers worked near a surf lifesaving IRB.
It also showed a semi-submerged boat near shore.
Aucklander Campbell Wright was on a boat going out fishing when he saw 20 to 30 people in the water trying to right the stricken vessel, which he believed was a pleasure boat about 5m long.
"There was a massive line of people trying to right the boat. It took a lot of people and a long time. There was a big cheer when they got it over."
Along with the rescue helicopters, two ambulances, two managers and a rapid response unit were sent to the Vista Paku area to help.
