A man and a woman, both international tourists, died when the Eurocopter 120 went down close to a Barrier Reef pontoon on Wednesday afternoon.
Three other people, including the male pilot and a male and female passenger, also believed to be from overseas, were taken to the mainland for treatment.
Whitsunday Air Services, the company behind the helicopter has suspended all operations following the crash as it works with authorities to determine the cause of the crash.
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Two dead in Whitsundays helicopter crash
"We are extremely saddened by this incident and our deepest condolences are with the families of all of the passengers," the company said in a statement.
"Whitsunday Air Services is continuing to work with the Queensland Police, the ATSB and CASA to assist with their investigations."
Whitsunday Mayor Andrew Wilcox says the local community was devastated by the crash.
"I know most of the tourism operators in the Whitsundays personally and I know they all hold their passenger experience and their passenger safety as their number one priority," he told ABC Radio.
"It will be sombre day for us in the Whitsundays. My thoughts and prayers at this stage are with the families affected by this."
The Australian Transport Safety Bureau confirmed a crash investigation was underway.
"A team of Transport Safety Investigators will soon travel to the accident location to commence the evidence collection phase of the investigation," an ATSB statement said.
"There, investigators will interview witnesses, examine any available recorded data, review operational records and technical documentation amongst other activities."
The pontoon, 65km northeast of the Whitsundays, allows underwater viewing chambers with tourist operators in the area saying Hardy Reef offers an excellent combination of reef, coral and fish life for tourists.
The well-known Heart Reef is also nearby.
Meanwhile, a man is in a critical condition in a Brisbane hospital after a helicopter crash in outback Queensland on Wednesday afternoon.
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