Investigators are piecing together how a seaplane crashed near a tourist island, leading to the deaths of three people and seriously injuring three others.

Police believe a privately owned Cessna 208 Caravan 675 aircraft struck a small limestone outcrop called Phillip Rock while taking off from Rottnest Island, off the coast of Perth, about 4pm on Tuesday.

It plunged nose-first into the water near Thomson Bay with seven on board including the pilot.

Three bodies were pulled from the wreckage by police divers on Tuesday night after a frantic search through the afternoon for the missing passengers.

The victims include a 65-year-old Swiss woman, a 60-year-old Danish man, and a 34-year-old male pilot from Perth.

Divers faced a challenging and confronting recovery of the deceased, who were discovered inside the wreckage eight metres below the water’s surface, Police Minister Paul Papalia said.

Four people were helped from the water after the crash, three of whom were taken to hospital with a range of injuries

The survivors include a 63-year-old Swiss man, a 63-year-old West Australian man, a 65-year-old West Australian woman and a 58-year-old Danish woman.

WA Police Commissioner Col Blanch said there were still parts of the wreckage submerged and authorities would be working to get everything out of the water.

He said there was a 200-metre exclusion zone in place while police and Australian Transport Safety Bureau (ATSB) officers conducted investigations and recovered the remaining parts of the aircraft.

Mr Blanch said the police investigation will look into how the three people died while the ATSB will investigate how the crash happened.

The agency has sent a team from Perth, Brisbane and Canberra who specialise in aircraft operations and maintenance and “human factors”, ATSB Chief Commissioner Angus Mitchell said in a statement.

The investigation will gather evidence including recovering aircraft components to be examined at the agency’s technical facilities in Canberra, interviewing survivors and witnesses, and collecting flight data and maintenance records.

Witnesses said the plane made a huge splash when it hit the water.

“It was just a big splash, it wasn’t a big explosion or anything crazy,” holidaymaker Hayden Harvey told The West Australian.

“It’s obviously like a sort of drop in the heart.”

Emergency services and civilian vessels rushed to the scene to help pull passengers from the plane.

WA Premier Roger Cook said his thoughts were with the family and friends of the victims but also thanked the first responders, including civilians, who rushed to help.

“They responded with true Western Australian spirit and the efforts undoubtedly save lives,” he said.

The images we are seeing of an emergency unfolding off Rottnest Island are deeply concerning.

The Cessna plane had been recently acquired by operator Swan River Seaplanes, which runs scenic flights around Perth and Rottnest Island.

The plane arrived on New Year’s Day after flying from NSW and remains registered to its previous owner Whitsunday Air Services Pty Ltd.

Rottnest Island, also known as Wadjemup, about 20km off the coast, is a popular holiday spot, attracting thousands of Australian and overseas visitors each year.