The Prince of Wales, 73, met recently with his 95-year-old mother, but the monarch is not displaying any symptoms, a Palace source said.
The source said the situation will continue to be monitored, but a running commentary would not be provided on the Queen's health.
WATCH: Prince Charles tests positive for COVID-19 for a SECOND time
It is not known when exactly the Prince met with the Queen. But he held an investiture on Tuesday at Windsor Castle, the day after the Queen returned to her Berkshire abode from Sandringham.
People who develop coronavirus symptoms are asked to notify those they have been in contact with in the previous 48 hours.
The Queen is understood to be fully vaccinated so will not need to self isolate, unless she tests positive. But she will be advised to take rapid lateral flow tests, one a day for seven days.
Clarence House confirmed in a tweet on Thursday: "This morning The Prince of Wales has tested positive for COVID-19 and is now self-isolating. HRH is deeply disappointed not to be able to attend today's events in Winchester and will look to reschedule his visit as soon as possible."
Aides said the future King was found to be positive during a routine test – which suggested he was experiencing no strong symptoms – but they declined to go into further details on his medical condition.
The Queen and Charles pictured in May 2021
Meanwhile, Charles's wife, Camilla, carried out engagements in west London on Thursday, with a spokesman confirming: "The Duchess of Cornwall has routinely tested negative today. She is on a separate series of engagements from the Prince of Wales."
During her outings Camilla said it is "lucky" she has tested negative after the Prince of Wales returned a positive result for Covid.
Speaking to Willie Hartley Russell, high sheriff for Berkshire, during a visit to Thames Valley Partnership, she said: "He's diagnosed now. Luckily [she's negative]. I've taken it so many times."
He added: "It gets a bit pointless, doesn't it?" and Camilla agreed.
The Queen marked the start of her Platinum Jubilee over the weekend
Speaking to the PA news agency afterwards, Mr Hartley Russell said: "She said, 'Yes unfortunately he had tested positive again'. I said he must be building up lots of antibodies.
"She said something like he's finding it a bit tiresome to have got it again, but she said it in a light-hearted way."
It comes after Charles and Camilla attended a reception at the British Museum on Wednesday evening to celebrate the work of the British Asian Trust (BAT), which he founded in 2007 to work to reduce poverty in south Asia.
In December, the couple confirmed that they had had their booster injections as they urged members of the public to do the same.
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