The RAF plane, which was carrying Prince Andrew, Prince Edward, and his wife Sophie, took off for Balmoral at 2.39 p.m. despite leaving at 1.30 p.m., according to The Sun.
The Dassault Falcon aircraft touched down at Aberdeen airport at 3:50 PM.
It is unknown why there was a last-minute hold-up at RAF Northolt in South Ruislip.
Because a disaster would have caused a constitutional crisis, Prince Harry was not aboard the aircraft and had to go independently to Scotland.
The Duke of Sussex is said to have been enraged when he arrived at Balmoral two hours after his adored grandmother passed away.
Thousands of mourners lined the route as the Queen’s coffin departed today for its 500-mile journey to Buckingham Palace from her beloved Balmoral Castle.
The RAF jet – which had Prince William, Prince Andrew, Prince Edward and his wife Sophie on board had taken off for Balmoral at 2.39pm despite being scheduled to leave at 1.30pm, reports say
Just after 5pm, a fleet of cars, including a Range Rover driven by William, with Andrew in the passenger seat and Edward and Sophie in the back, arrived at Balmoral
Royal author Brian Hoey said: ‘There is a strong constitutional reason that William and Harry do not fly together — and that is to do with the line of succession.
‘Royal aides have to consider everything, and this is very likely to have been a factor.
‘While events happened very quickly, they have had years to plan for all eventualities.’
Mr Hoey, a constitutional expert, also said that the ‘speed of events’ had caught everyone off-guard and it could have affected travel plans.
Prince William’s wife Kate had stayed at Adelaide Cottage to collect their children George, Charlotte and Louis from their first day at school while her husband flew to be with his grandmother.
The Sussexes had announced at 1.50pm that both Harry and his wife Meghan would be travelling to Scotland, but at 4.40pm clarified that Meghan would be staying behind.
They had been staying at Frogmore Cottage after flying over from the US for a series of charity events in London, Manchester and Germany.
At 12.32pm, Buckingham Palace issue a statement saying doctors were concerned for the Queen’s health.
Left to right: William, Prince of Wales, Catherine, Princess of Wales, Prince Harry, Duke of Sussex, Meghan, Duchess of Sussex, wave at well-wishers on the Long walk at Windsor Castle on September 10
At 6.31pm, Buckingham Palace say in a statement: ‘The Queen died peacefully at Balmoral this afternoon’
They said the head of state was comfortable and royal physicians recommended she stays under medical supervision as the future king, the Prince of Wales, and second in line to the throne, the Duke of Cambridge, cleared their diaries to dash to the Queen’s Aberdeenshire home.
At 12.45pm, Clarence House said Charles and the Duchess of Cornwall had travelled to Balmoral. A minute later Kensington Palace confirmed William would also be travelling north.
At 2.39pm, Royal Air Force flight KRF23R took off from RAF Northolt in South Ruislip, west London, according to flight tracking website Flightradar24.com.
The plane was carrying William, the Duke of York, and the Earl and Countess of Wessex.
At 3.50pm the plane, a Dassault Falcon, landed at Aberdeen airport.
Just after 5pm, a fleet of cars, including a Range Rover driven by William, with Andrew in the passenger seat and Edward and Sophie in the back, arrived at Balmoral.
At 6.31pm, Buckingham Palace say in a statement: ‘The Queen died peacefully at Balmoral this afternoon. The King and The Queen Consort will remain at Balmoral this evening and will return to London tomorrow.’
Just after 7pm, Charles, who became King on the death of his mother, said: ‘The death of my beloved mother, Her Majesty The Queen, is a moment of the greatest sadness for me and all members of my family.
‘We mourn profoundly the passing of a cherished sovereign and a much-loved mother. I know her loss will be deeply felt throughout the country, the Realms and the Commonwealth, and by countless people around the world.
‘During this period of mourning and change, my family and I will be comforted and sustained by our knowledge of the respect and deep affection in which the Queen was so widely held.’
At 7.08pm, Prime Minister Liz Truss said it was ‘the passing of the second Elizabethan age’ and concluded an address by saying ‘God save the King’.
She refers to Charles, the new King, as King Charles III, saying: ‘Today the Crown passes, as it has done for more than a thousand years, to our new monarch, our new head of state, His Majesty King Charles III.’
At 7.25pm, Clarence House confirmed that Charles would be known as King Charles III.
At 7.41pm, Kensington Palace confirms that Kate and William will be known as the Duke and Duchess of Cornwall and Cambridge.