During the summer of 1988, when the family was on vacation to Balmoral's castle, the monarch could no longer control her disapproval of her son's extramarital relationship and confronted him about it.
The explosive claims were revealed in Rebel Prince: The Power, Passion and Defiance or Prince Charles, the latest book by the self-proclaimed royal author Tom Bower.
Mr. Bower said: "She would not condone his adultery nor forgive Camilla for not leaving Charles alone to have his marriage restored."
The British journalist claims that the prince had approached his mother about the opportunity to welcome Camilla into the royal family – despite the fact that she was married to Princess Diana.
The monarch angered the first-in-line request to the throne and the conversation ended with Charles calling his beloved Camilla and told her by tears about the news.
The book concentrates on the relationship between the Queen and her daughter-in-law, the Duchess of Cornwall, and claims that after twenty years it has never blossomed.
After Prince Charles married Diana Spencer in 1981, he got an affair with Camilla Parker-Bowles, which he knew since his only days.
In a TV interview in 1995, when she talked about her problematic relationship with Prince Charles, the princess declared: "Well, there were three of us in marriage, so it was a little busy."
In 1996, the couple was officially separated, a year before Diana died tragically by a car accident in Paris.
In 2005, Prince Charles married his long-term partner Camilla during a civil ceremony.
The claims come after the Netflix documentary "The Royal House of Windsor" suggested that the Queen Mother had no problem with Charles who had an affair.