In a statement realeased on Friday, Rome said the church would instead be represented by a senior official who acts as the Vatican’s representative on foreign affairs at Monday’s ceremony.
“The Most Reverend Paul Gallagher, secretary for relations with states and international organisations, will represent Pope Francis at the funeral of Her Majesty Queen Elizabeth II,” said the Vatican.
Earlier this week, Pope Francis sent a message of condolence to Britain’s new head of state, King Charles III.
He said: “Deeply saddened to learn of the death of Her Majesty Queen Elizabeth II, I offer heartfelt condolences to Your Majesty, the Members of the Royal Family, the People of the United Kingdom and the Commonwealth.”
The Queen and the Pope met in Italy in 2014.
She presented the pontiff with a hamper of British food, including 12 eggs from the crown estate and the pair had a meeting lasting around 20 minutes.
Queen Elizabeth did not attend Pope Francis’ inauguration in March 2013, sending the Duke of Gloucester as a representative.
She made her first visit to the Vatican in 1951, and met Pope Pius XII.
The Queen, who celebrated the 70th year of her reign this year, passed away aged 96 on Thursday 8 September at Balmoral.