Her Majesty, who turns 94 next month, was chauffeured to Windsor Castle after Cobra crisis talks on Thursday.
It comes as the government announced on Saturday that ten more people have died, bringing the UK total to 21, with confirmed cases soaring to 1,140.
Plans are in place to quarantine the Queen and Prince Philip, 98, at Sandringham if the outbreak worsens.
A royal source told the Sun that Her Majesty is "in good health but it was thought best to move her".
The source said: "A lot of her staff are a bit panicky over coronavirus. The Palace hosts a constant stream of visitors including politicians and dignitaries from around the world.
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“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 Palace has around 500 staff, while Windsor only has about 100.
The Queen has cancelled several public events "in the coming weeks" due to coronavirus, the palace announced on Friday.
In the midst of spiralling cases of the highly infectious bug in the UK and the rest of the world, Buckingham Palace said it is taking "a sensible precaution" in amending the monarch's diary.
A statement read: "As a sensible precaution and for practical reasons in the current circumstances, changes are being made to The Queen’s diary commitments in the coming weeks.
"In consultation with the Medical Household and Government, Her Majesty’s forthcoming visits to Cheshire and Camden will be rescheduled. Audiences will continue as usual. Other events will be reviewed on an ongoing basis in line with the appropriate advice."
Visits to the Camden area of London and to Cheshire in northwest England have been cancelled.
"In consultation with the medical household and government, Her Majesty’s forthcoming visits to Cheshire and Camden will be rescheduled," the Palace said. "Audiences will continue as usual."
Meanwhile Prince Charles and his wife Camilla have cancelled an upcoming tour of Bosnia, Cyprus and Jordan on British government advice, a spokesman for the royal couple said on Thursday.
"Owing to the unfolding situation with the coronavirus pandemic the British government has asked their royal highnesses to postpone their Spring tour," a spokesman said.
This isn't the first measures that have been taken to protect Queen Elizabeth from the deadly virus; last week at an investiture at Buckingham Palace - where she hands out honours such as MBEs - the monarch was photographed wearing gloves, which is not something she typically does.
On Sunday, health secretary Matt Hancock confirmed the government will tell people over 70 to stay at home for up to four months to keep them safe from the virus, as he admitted on Sky News that the NHS does not currently have enough ventilators for the fight against coronavirus.
The elderly will be told to self-isolate even if they do not have symptoms in a bid to stem the spread of the disease and protect the most vulnerable in society.
He said: “We don't want to do that too soon because clearly it is not an easy thing to do, it is not an easy thing to sustain' but he said he expected the stay-at-home advice to be issued 'certainly in the coming weeks absolutely.”