The 86-year-old monarch, usually visits St Mary Magdalene Church every Sunday while staying at her home in Norfolk.
She is still expected to attend church on Christmas Day and her Christmas message was pre-recorded, so it will still go out on Tuesday.
A spokeswoman said: "We are expecting business as usual next week."
Mary Relph, 78, said that since 1988 she has waited outside the church whenever the monarch has attended a service there, so as to see the Queen.
"I don't remember her ever missing it," she said. "I remember her going around the back once. I am disappointed but I hope she is OK," she told the BBC.
The Duke of Edinburgh, 91, walked the few hundred yards from the house to the church accompanied by the Duke of York, the Earl and the Countess of Wessex and their daughter Lady Louise and Princesses Beatrice and Eugenie.
The Queen traditionally spends the festive period with her family at her at her Norfolk estate.
This year Prince William and his pregnant wife Kate are planning to spend Christmas at the Middleton family home.
On Saturday, St James's Palace said the couple will to spend the day privately in Bucklebury, Berkshire, but they plan to visit Sandringham at some point over the festive period.
And Prince Harry is currently serving as an Apache pilot in Afghanistan.
The Queen's Christmas Day broadcast to the UK and Commonwealth has been recorded in 3D for the first time.
