The head of state, who has recently recovered from a bout of Covid, hoped to join Charles, the Duchess of Cornwall and the Duke and Duchess of Cambridge at the important occasion in the royal calendar.
But a Buckingham Palace spokesman said: “After discussing the arrangements with the Royal Household, the Queen has asked the Prince of Wales to represent Her Majesty at the Commonwealth service at Westminster Abbey on Monday.
“The Queen will continue with other planned engagements, including in-person audiences, in the week ahead.”
The spokesman revealed another member of the royal family had contracted Covid after the Queen, Charles and Camilla all recently tested positive for the virus and later returned to royal duties.
He said: “The Duke and Duchess of Gloucester will no longer attend, following the duke’s positive test for Covid.
“The Queen’s Commonwealth Day message will be distributed in the usual way.”
The Queen’s decision not to attend the service is likely to be interpreted as a precautionary measure by royal commentators and a practical move, rather than a new health issue.
She now regularly uses a stick and recently commented about her mobility issues, telling two senior military officers during a Windsor Castle reception “Well, as you can see, I can’t move,” when asked how she was.
With the Queen due to celebrate her 96th birthday in under six weeks, maintaining her comfort is a consideration and it is understood she has been pacing herself, although the head of state was keen to do what work she could during her bout of Covid.
The service would have been the Queen’s first major public appearance since reaching her Platinum Jubilee milestone.
She last pulled out of attending the service nine years ago in 2013 while recovering from a nasty bout of gastroenteritis.
Before that, the Queen had not been absent from a Commonwealth Day Observance service for 20 years, the last occasion being when she had flu in 1993.
She returned to in-person events on Monday, after contracting the virus, when she welcomed Canada’s prime minister Justin Trudeau to Windsor Castle for an audience.
During her meeting with Mr Trudeau, the head of state was not pictured with the walking stick she has been using of late and the pair shared a joke at the start of their meeting.
The monarch tested positive for Covid on February 20 and Buckingham Palace said at the time she was experiencing “mild cold-like symptoms”.
The Queen last met a group of people in public on February 5, the eve of reaching her Platinum Jubilee, when she hosted a reception at her Sandringham home for local charity workers, volunteers and former staff from her Sandringham estate.
Concerns were raised about the Queen’s health when she spent a night in hospital last October, missed a string of events and was advised to undertake light duties by royal doctors.
She had only returned to something approaching normal working practices just before contracting Covid-19.
During the Commonwealth Day service, the 1,500-strong congregation will include Princess Alexandra, Prime Minister Boris Johnson, Commonwealth secretary-general Baroness Scotland, high commissioners, ambassadors, senior politicians and dignitaries from across the UK and Commonwealth, faith leaders and more than 600 schoolchildren and young people.
The service will feature the world premiere of the musical piece Beacon Of Brightest Light, inspired by the Queen’s Platinum Jubilee, composed by Debbie Wiseman.
The event will begin with a procession of Commonwealth flags and members of the royal family will meet people involved in the service at the end.
Organised by the Royal Commonwealth Society, the event will feature the Queen’s Commonwealth Day message.