Up to 400 were evacuated from the DoubleTree by Hilton on Cairns Esplanade after the crash, which set the top of the building alight, shortly before 2am today, police said.
"Nautilus Aviation are working closely with Queensland Police, the Australian Transport Safety Bureau and other authorities as they investigate the unauthorised use of one of our helicopters in the early hours of this morning.
"As we continue to fully support the ongoing investigation, we will not be making further comments at this time."
Forensic investigators are working to identify the pilot, who died at the scene. They were the only person in the helicopter, police said.
Two other patients — a man in his 80s and a woman in her 70s — were taken to Cairns Hospital in a stable condition.
Hotel guest Alastair Salmon woke up to "a colossal ear-deafening bang". He and roommate Harry Holberton were on the third floor.
Mr Holberton said the crash felt like a bomb going off, with flames "rising up the side of the building".
"Suddenly all the alarms start going off and then [] start evacuating with police yelling 'get out, get out, get out'."
Mr Salmon, who had travelled from London, said he first mistook the helicopter's rotor blade for a lamppost.
"Then we looked up there and you could see this massive hole in the window of the building," he said.
The pair were let into the hotel to get their belongings.
"All over the hotel there was debris, parts of a windscreen," Mr Holberton said.
Mr Salmon said he could see "small fragments of what looked like a helicopter" in the hotel's courtyard.
Wayne Leonard, who lives 100 metres from the hotel, said he woke up to a bang.
"It was very loud — I thought it might have been a tower on top of the building exploding, it was that sort of a sound," he said.
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