Brad Sorrell, the regional commander of WA police, said while there were no life-threatening injuries, 12 people had been seriously hurt in the incident, with several thrown into the crocodile-infested waters.
Sorrell would not comment further about what caused the accident as a multi-agency investigation had already been launched.
More injured passengers were expected to arrive in Perth after dark this evening.
Those people who fell in the water, which is also home to the deadly box jellyfish, were winched by helicopter to a large pontoon before being flown to a makeshift triage area set up at the nearby Koolan Island iron ore mine.
Damien Whitham, the critical incident controller of the Royal Flying Doctor Service, said four aircraft with six doctors and six nurses were sent to the remote area. Those people with serious injuries were then airlifted to Royal Perth hospital.
The RFDS assessed and treated passengers on the boat and nine people were treated for minor injuries. No children were involved, he said.
Those with minor injuries began arriving in Broome by seaplane at around noon today.
First responders reached the boat by 8.30am, Whitham said.
Hospitals in the northern half of the WA Country Health service network were told to prepare for the arrival of up to 25 patients.
The boat was operated by Horizontal Falls Seaplane Adventures, a Broome-based tourism company that charges about $1,000 for a scenic flight, Talbot Bay cruise and ride through the falls.
In a statement, the company said the boat was guided by an experienced skipper but was involved in an incident early this morning.
Inspectors from the Australian Maritime Safety Authority were expected to arrive tomorrow.
WorkSafe was also investigating.
