The queen and Prince Philip had joined other royals in attending the traditional New Year's Day service at the Church of St. Mary Magdalene on the estate hours before the discovery was made.
The royals have not spoken publicly on the discovery, but police reportedly alerted them to the discovery Monday night.
"My understanding is that the queen is being kept informed of these developments when there is news to tell her," Duncan Larcombe, royal editor for the UK's Sun newspaper, told ABC News.
The Queen and Prince Philip have not announced plans to leave the estate due to the discovery, instead, for now, choosing to remain through to their planned February departure.
The grounds surrounding the queen's residence at Sandringham are particularly busy this time of year with extra security personnel on hand to guard the royal family from the flock of tourists who travel to the estate in hopes of catching a glimpse of the family.
While the murder investigation might be the first to happen directly on the grounds of a royal palace, the storyline is eerily similar for the queen and her family.
The body of Robert James Moore, a U.S. man described as a loner and obsessed with the queen, was discovered in March on an island in St. James's Park near Buckingham Palace, roughly three years after Moore was believed to have died.