Nautilus Aviation said the person who flew the helicopter had been an employee for four months in a ground crew position.
The charter company said the person had a New Zealand pilot's licence but had never flown in Australia and was not authorised to use a Nautilus Aviation helicopter.
"Nautilus Aviation have now received confirmation from the Queensland Police Service as to the identification of the individual who gained unauthorised access to our helicopter hangar and misappropriated one of our helicopters," the company said in a statement on Tuesday.
Nautilus Aviation confirmed the person had been given a farewell party by employees on Sunday night.
"We can confirm this event did occur and was a privately organised send-off for the individual involved in Monday morning's incident, who was recently promoted to a ground crew position at another one of our bases," the statement said.
"This was not a work event and was co-ordinated by friends."
A helicopter left on an "unauthorised" flight from Nautilus Aviation's hangar at Cairns airport early on Monday morning, crashing into a hotel roof about 2am.
The pilot - the sole occupant - died after the helicopter struck the roof of DoubleTree by Hilton in Cairns' CBD, prompting the evacuation of hundreds of guests.
Two guests - a man in his 80s and a woman in her 70s - were taken to hospital for smoke inhalation and have been released.
Nautilus Aviation said it would let police release the person's identity.
The company said it had completed interviews with the Australian Transport Safety Bureau and police, cooperating with "full transparency" about the events.
"We offer our heartfelt condolences to the individual's family and all who have been affected by this tragedy and continue to offer our support to our employees during this very challenging period," the statement said.
"We ask that the media respect the privacy of our employees during this time."
Investigators resumed work on Tuesday in a bid to shed light on the circumstances after the helicopter's wreckage was removed from the hotel.
Authorities had previously declined to say if the pilot had a licence or how the helicopter was flown out of Cairns airport without authorisation.
The helicopter was seen flying for at least five minutes in the Cairns CBD before it crashed into the hotel roof, smashing the windows of nearby rooms with one occupied by a sleeping elderly couple.
An aviation expert said night flying required more concentration and could have contributed to the crash.
"If it was an accident, it probably was a factor that it was in darkness," aviation lawyer Peter Carter told AAP.
Investigators had hoped to know more about the flight after recorded data from the helicopter was sent for analysis.
Propellers were dislodged when the helicopter hit the roof with one landing on the street outside and the other in the hotel pool while still on fire, prompting the evacuation of up to 400 guests.
Australian Transport Safety Bureau Chief Commissioner Angus Mitchell said it was "miraculous" that no one else was hurt.
"It certainly could have been a lot worse," he told ABC Radio.
