Sir Christopher Geidt said to have left heir apparent furious over speech.
A power struggle between Buckingham Palace and the Prince of Wales led to the Queen's most senior courtier being forced out of his job, it has been reported.
Sir Christopher Geidt, the Queen's private secretary, raised eyebrows when he suddenly announced in July he was leaving after 15 years of royal service.
At the time he gave no indication of any discord, instead praising the Queen and insisting the royal family was united behind the long-serving monarch.
But a report in The Times paints a different picture of what was happening behind the scenes.
Sources speaking to the newspaper claim the 56-year-old was in reality forced out following complaints by Prince Charles and his brother, the Duke of York.
The unprecedented ousting – the first time the Queen has got rid of her private secretary – was said to be the climax of rising tensions between the two royal households over how to manage the handover of power between the monarch, now 91, and her heir.
Staff working for Prince Charles, the longest-serving heir apparent in British history, were keen to increase his involvement in key royal events by the time he reaches 70 in November next year.
Reportedly referred to as "Project 70", the prince's team wanted this to include the Royal Maundy service and Commonwealth events. One source told the newspaper it would "show that he is the king in waiting."
But Prince Charles was said to have become "infuriated" after a speech Sir Christopher gave to 500 royal staff in May, announcing the retirement of the Duke of Edinburgh from public life, and also calling for the royal households to unite in support of the Queen. It was said to have been viewed by the prince and his staff as "presumptuous".
"Charles was told about this, was furious, and went to see his mother," one source claimed. The message was: "This is just not possible, and Geidt has got to go."
The ultimatum came after many years of tensions between Buckingham Palace and Clarence House, the official residence of Prince Charles.
Prince Andrew reportedly backed his brother in the row, having held a grudge against Sir Christopher over the role he played in forcing him to step down as trade ambassador in 2011 due to his friendship with convicted sex offender Jeffrey Epstein.
Sir Christopher was allegedly told by Earl Peel, the lord chamberlain, that his position was untenable, and he resigned in July. While he publicly denies being forced out, Sir Christopher is said to feel "bruised" by what happened and believes the Queen failed to support him.
The Times suggested his removal will mean greater control for Prince Charles over the pace of preparations for his accession to the throne, including the takeover of Balmoral and Sandringham estates.
A joint statement by Buckingham Palace, Clarence House and Kensington Palace said: "While we never comment on the confidential employment details of individuals, it was previously announced in July that Sir Christopher Geidt is stepping down after ten years as private secretary.
"At the time of the announcement, the lord chamberlain paid tribute to the major contribution made by Sir Christopher, who in turn commended the support offered to Her Majesty by other members of the royal family.
"Recent years have seen an ever-closer working relationship between all the different royal households and their respective teams. The Prince of Wales and the entire royal family are committed to supporting the Queen in whatever way they can at Her Majesty's request. Beyond that, we are not going to engage with a story based on rumours from unnamed sources."