The British tourist was on his second dive of the day when the incident happened.
Crew onboard the Silversonic boat, operated by tour company Quicksilver, called emergency services and unsuccessfully tried to revive him with a defibrillator.
A doctor was flown to a helipad at the reef where he met the dive boat and assisted with CPR but was unable to save the man, who was travelling with his wife.
'CPR was performed on a male patient in his sixties by a nurse on board a vessel and subsequently by a doctor,' a Queensland Ambulance spokeswoman said.
The Association of Marine Park Tourism Operators (AMPTO) said the alarm was raised when the diver was spotted without a regulator in his mouth 15m (49ft) below sea level on the ocean floor.
The incident comes just two days after two elderly French tourists Jacques Goron, 76, and Danielle Franck, 74, died while snorkelling on Wednesday at Michaelmas Cay, also near Cairns.
Both had pre-existing medical conditions and it is believed both suffered heart attacks.
However an Australian cardiologist, Ross Walker, had speculated whether they were stung by highly venomous Irukandji jellyfish.
He said: 'Irukandji are the size of your little fingernail, they're very small, you can't see them. Let's look at fact and probability. It's highly unlikely that two people are going to die within minutes of each other just because they've got underlying medical conditions.'
Peter Fenner, an expert on the jellyfish, agreed the French couple may have been stung, telling The Cairns Post: 'The possibility does exist that it may have happened, with the sting creating very high blood pressure, which would then cause damage to the heart and arteries.'
But tour operators insisted there was no sign of jellyfish at the scene.
Alan Wallish, from the firm which operated the Passions of Paradise vessel on which the French pair died, said: 'We don't get Irukandjis at this time of year and the two parties were very separate.
'The lady was 15 metres away from the boat... [She] had a full stinger suit on. I really can't see how jellyfish or stingers would have contributed in any way.'
AMPTO executive director Col McKenzie said the week was as bad as he could remember.
'I can't remember how long ago it is since we have multiple fatalities at the same time,' Mr McKenzie told Daily Mail Australia.
'It might have been 1988 or even 1987 when we had a few fatalities in the same week.
'In this instance they were all older people, this diver is 60, the other two were in their mid-70s - what are the odds of something like this happening?'
The Silversonic dive boat has operated for 11 years and carried 230,000 divers during that time with no diving fatalities.
The death of the British man on Friday means ten people have been killed in the water of Far North Queensland since February.
A spokesman for the Foreign Office told MailOnline: 'We are in contact with the local authorities following the sad death of a British national on the Great Barrier Reef in Queensland and we are providing assistance to the family at this difficult time.'
'We're not sure as to what has happened at this stage,' a Quicksilver spokeswoman added.