Emergency crews were called at about 2 a.m. (1600 GMT on Sunday) after the twin-engine helicopter hit the roof of the hotel, setting part of the structure on fire and triggering the evacuations, Queensland state police said in a statement.
Police said the helicopter had been taken from its hangar at Cairns airport for an "unauthorised flight", but did not elaborate. The pilot, who has yet to be identified and was flying alone, was declared dead at the scene.
Police said the flight was an isolated incident and there was no threat to public safety. They added that the pilot's intent was unknown, as was the manner in which the aircraft was taken.
The crash took place at Hilton's HLT.N Double Tree Hotel in Cairns, a gateway city on the route to the Great Barrier Reef, staff at its reception desk said. At 5:30 p.m. (0730 GMT), it was still closed, with guests moved elsewhere, they added.
Two hotel guests, a man in his 80s and a woman in her 70s, were discharged after being taken to hospital, state broadcaster ABC said, adding that two of the helicopter's rotor blades came off, with one landing in the hotel pool.
The forensic crash unit will work with Australia's transport safety regulator to establish the details, police said.
Helicopter owner Nautilus Aviation said it was co-operating with police investigating the unauthorised use of the craft.
