BBC royal correspondent Nicholas Witchell says the prince and his wife flew to Scotland on Sunday, although they did not travel on a scheduled flight.
He adds that they were both tested on Monday and got their results last night.
Prince Charles's last public engagement was on 12 March - the same day he last saw his mother, the Queen. Palace officials say the Monarch remains in "good health".
The prince, 71, and his wife, the Duchess of Cornwall, 72, are self-isolating at Birkhall on the Balmoral Estate in Aberdeenshire.
A Palace statement said: "The tests were carried out by the NHS in Aberdeenshire where they met the criteria required for testing."
CGTN's Asieh Namdar and Dr. Alok Patel discuss racial injustice in society and in the health care system. CGTN's Asieh Namdar and Dr. Alok Patel discuss racial injustice in society and in the health care system. Dr. Michael Osterholm discusses a spike of coronavirus cases in states across the country as rates decline in other states. Dr. Osterholm says we are still 'in this thing for months.' Aired on 06/16/2020. The president who repeatedly played down the coronavirus outbreak is now in quarantine at his home in Brazil after testing positive.
Jair Bolsonaro has cancelled his schedule for the next few days but insists he is still in good health.
He is one of nearly 1.7 million people infected in Brazil, the second-worst affected country in the world.