Alex Salmond’s coffin was draped in a Saltire ahead of the plane bringing him home to Scotland taking off.
Mr Salmond died on Saturday from a heart attack while speaking at a conference in the city of Ohrid in the country’s south west.
The flight, which was chartered by an unnamed private individual, took off from Ohrid St Paul the Apostle Airport just after 10.20am UK time.
Mr Salmond’s body will return to the north east of Scotland, close to his home in Strichen, Aberdeenshire, and the seats he represented at both Westminster and Holyrood, this afternoon.
Plans are being put in place for for a private family funeral along with a more public memorial service.
Former SNP MP and Alba Party chairwoman, Tasmina Ahmed-Sheikh, attended the coffin before it was taken to the plane, which was paid for by businessman Sir Tom Hunter.
Ms Ahmed-Sheikh draped Mr Salmond’s coffin in the Saltire – which is understood to have been provided by the Scotland Office – as it was taken from a van on the tarmac.
Mr Salmond’s body was carried by six members of the North Macedonian military to the flight, along a red carpet which was flanked by eight other soldiers standing at attention, to the sound of a trumpet.
The soldiers, flight and ground crew observed a moment’s silence before Mr Salmond’s body was loaded onto the flight.
A Downing Street spokeswoman said: “The Prime Minister’s thoughts are with his friends and family today.”
The spokeswoman also urged people to respect the family’s calls for privacy.
The Salmond family were in talks with the UK and Scottish Governments about the best way to repatriate the former SNP leader’s body.
His friend and Tory MP, Sir David Davis, had pushed for the RAF to be used to bring his body back.
But the decision was taken, instead, to use a private charter paid for by Sir Tom.
The businessman said on Thursday: “Whilst he and I disagreed on some of his ambitions, Alex Salmond devoted his life to Scotland and the Scottish people and, as such, he – and importantly his family – deserved the dignity and privacy of a private return to the home of his birth.
“Our deepest sympathy and thoughts are with his family at this time.
“To be clear, I remain resolutely apolitical.”
Kenny MacAskill, who stepped in after Mr Salmond’s death to take over as the acting leader of the Alba Party, said: “The family are incredibly grateful for the support which is being provided by a private citizen to charter a private plane to allow Alex’s body to come home to Scotland.
“It brings a great deal of comfort to Moira and other members of the family to know that he will soon be home with them.
“The family have asked that their privacy be respected at this time and will be making an announcement in due course about the funeral arrangements and a memorial service to honour the life of Alex Salmond.”
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