It has been widely reported that the Queen would boycott the ceremony in the Guildhall because she did not want to attend a humiliating "town hall" service, but the real reason can now be revealed.

The Queen privately disapproves of the 33-year on-off relationship between Prince Charles and Mrs Parker Bowles and feels that her eldest son has put personal concerns before duty. The Queen's friend told The Telegraph that Her Majesty had been disappointed that her decision not to attend the wedding had been portrayed as a "snub" to the couple when this is not the case. "The Queen feels she has to put her role with the Church before her role as a mother," said the friend.

A senior royal official said: "The Queen takes her position as Supreme Governor of the Church of England incredibly seriously. She also has great personal faith."

Three senior courtiers told The Telegraph this weekend that the Queen had already informed Prince Charles that she would not be attending the civil ceremony even when he planned to hold it within Windsor Castle. The venue was switched in late February because of problems with using the castle.

One senior royal aide said: "The venue was never the issue for the Queen. The civil nature of the service is the issue. She did not feel it was appropriate for her to attend."

The Queen is attending the later service of dedication conducted by Dr Rowan Williams, the Archbishop of Canterbury. She is also hosting a wedding reception for more than 700 guests.

Royal officials do not believe that the Queen has ever attended a civil wedding service during her 53-year reign. It is also believed to be the first time that an heir to the throne has been married in a civil service. Some constitutional lawyers have questioned whether it is legal.

The explanation from Buckingham Palace about the non-attendance of the Queen and Prince Philip is that Prince Charles and Mrs Parker Bowles wanted a "low-key" ceremony. This has always been unconvincing, particularly after it was announced that the Princess Royal, the Duke of York and the Earl of Wessex would attend. One senior royal aide said that the Queen felt it would be undignified to spell out in a public statement her personal reasons for not attending the wedding. It might also be seen as implied criticism of Prince Charles, who will be the next Supreme Governor of the Church of England when he becomes king.

Hugo Vickers, a prolific author on the Royal Family who is writing a biography of the late Queen Mother, said that the Queen had never, to his knowledge, attended a civil ceremony.

"She is quite right not to attend - she is the head of the Church of England, after all. It never occurred to me that she would attend the register office ceremony and when people talk about it being a snub, it's nonsense. A snub is when no member of the Royal Family attended the marriage of the Duke and Duchess of Windsor in Paris in 1937."

The Queen attended the second marriage of Princess Anne to Cdr Tim Laurence at Craithie Church, near Balmoral, in 1992 because it was held within the Church of Scotland, which had more relaxed rules on divorcés marrying in church.

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