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The aircraft burst into flames after it came down at about 4.10pm in woodland near McRae's family home in Jerviswood, Lanark, killing everyone on board.
Police have now confirmed that four bodies were found inside the wreckage of the helicopter that was owned by McRae.
Colin McRae
Colin McRae was awarded an MBE in 1996
They said he was believed to be onboard the aircraft, but added formal identification was still to take place.
Campbell Roy, a member of McRae's management team, added: "I haven't had anything confirmed and at the moment it's speculation. I'm waiting to speak to the family to find out exactly what's happened."
However, Jean-Eric Freudiger, McRae's agent, told The Sunday Telegraph he had spoken to the driver's brother and he had confirmed the former champion had been piloting the Squirrel aircraft.
Speaking from his home in Switzerland, Mr Freudiger said he was still in shock and fighting back tears as he said he could not reach Mr McRae's wife, Alison.
He added: "I have heard that it was his aircraft. He was in the helicopter. I cannot believe it was a helicopter pilot error because as my best friend and the godfather of my daughter I know he was a very safe pilot.
"We have been close business partners and friends for seven years. He is the best person I have ever met in my life. I have to try and understand what I have just been told."
The aircraft is understood to have came down about a mile from Mr McRae's home at Bellefield Road.
The 39-year-old McRae - who has two children, Hollie and Johnny - became Britain's first World Rally Champion in 1995 and was still competing in the sport.
His father, Jimmy, was a five-time British rally champion, while his younger brother, Alister, is also a professional driver. Mr McRae has said he uses his helicopter, as well as a six-seater jet, to travel between his homes in Scotland, Monaco and Majorca.
He once told reporters: "I don't have things for show. I'm not brash and I'm not on an ego trip. If I buy something it is because I genuinely want or need it."
Squirrel helicopters can carry up to six people and police were last night unable to say how many people were on board.
A spokeswoman for Strathclyde Police said: "There is at least one dead and no one survived the crash. We don't yet know how many people were on board."
The crash was witnessed by a farmer. The aircraft was so badly damaged by fire that police could not initially identify what type it was.
The Scottish Ambulance Service confirmed that its own helicopter had been despatched to the scene along with three ambulance crews.
Strathclyde Fire Brigade also sent units to the scene.
The RAF spokesman added that its helicopter was on stand-by to assist. Police have cordoned off the area and the Air Accident Investigation Branch has been informed.
A spokesman for the British Airports Authority said the helicopter did not come from Glasgow or Edinburgh Airports.
Earlier this year, four people were killed when a Squirrel helicopter crashed in Cambridgeshire.