Aside from visitors to the palace, there are approximately 500 staff at Buckingham Palace, 100 working in Windsor, while only a handful work in Sandringham.
"She is weeks away from her 94th birthday and advisers believe it is best to get her out of harm's way," the source said.
"Buckingham Palace is in the middle of London and also has a bigger staff than other estates so is deemed a much more dangerous location.
"There have been no specific scares or positive tests there yet but no one wants to take any chances."
The Queen's shift to Windsor is not the only precaution being taken.
There are discussions of moving the court permanently during the crisis, and upcoming events possibly postponed or cancelled. This includes Palace garden parties in May and June, to which over 30,000 guests are invited.
A Palace spokesperson said "Future events will be reviewed on an ongoing basis, taking into account the appropriate advice."
Currently, there are over 1,100 confirmed cases of coronavirus throughout the UK, with the death toll sitting at 21.
Health officials expect the number of cases to skyrocket over the coming weeks, and are discussing strict measures, including placing people over 70 in strict isolation for four months.