It is thought that the encounter, reported in The Times, happened at the Monarch’s official London residence Buckingham Palace .
It is also believed that it happened several years ago and that the 90-year-old Queen is now unlikely to be found on similar expeditions.
In 2013 Prince Andrew was mistaken for an intruder and confronted by armed police as he walked in the Buckingham Palace garden.
Police said no weapons were drawn but issued an apology to the prince.
Managing Editor of Majesty Magazine Joe Little said about the tale of The Queen and guardsman: “What a great story.
“While wanting to take it with a pinch of salt, if Prince Andrew’s identity can be challenged by a policeman in the same garden in broad daylight then there’s no reason to think that something similar couldn’t happen to his mother in the dead of night.”
Usually taking the train to and from Kings Lynn to get to her Norfolk retreat, this Christmas she broke with tradition and was taken by helicopter suffering from a “heavy cold”.
She has been recovering inside Sandringham House since, missing the Christmas Day church service for the first time in almost 30 years and the New Year service the following week.
Concerns were raised for her health, however aides said she was “up and about” and receiving her usual Red Boxes of Government papers.
On Tuesday The Queen received Page of the Chambers Ray Wheaton at Sandringham where she invested him with the Insignia of a Lieutenant of the Royal Victorian Order, a personal honour recognising services to the Monarch.