Writing on Twitter, ITV’s Royal Correspondent Chris Shipp said Mr Johnson met the monarch between the search for new ministers and the firing of Minister Michael Gove. Mr Shipp asked “what the hell” the Queen and Mr Johnson were discussing as Downing Street is in complete disarray after a mass uprising from Conservative MPs.
He said: “Boris Johnson had his weekly audience with the Queen tonight (between the search for new ministers and the firing of Michael Gove).
“You wonder what the hell the Queen and Prime Minister were talking about or really what they asked him about what’s happening to Her Majesty’s government tonight?”
The Queen stayed at Wood Farm, a five-bedroom cottage on the Sandringham Estate in Norfolk.
However, on Wednesday morning she was seen returning to Windsor Castle, which is now her primary residence.
Despite a number of health problems in recent weeks, including ongoing mobility issues, Her Majesty appeared to be in good health.
However, it is believed that the monarch held her meeting with the prime minister on the phone.
The Queen no longer lives permanently at Buckingham Palace, which is just a short distance from Downing Street.
Royal reporter Cameron Walker confirmed the news on Twitter.
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It comes just weeks after the prime minister won a confidence vote from the parliamentary Conservative party.
Under current rules, Mr Johnson cannot be challenged with a new confidence vote for nearly 12 months.
Mr Johnson has dramatically fired Mr Gove on the phone after his Brexit colleague allegedly told him to resign, the state reports.
Supporters of the Prime Minister have labeled the Surrey Heath MP as a “snake”.
Mr Johnson has remained defiant against the former mayor of London, who is adamant he will not resign.