A Palace source told the BBC that the Duke and Duchess of Sussex did not ask the Queen about naming their baby Lilibet.
The source refuted claims that Prince Harry and Meghan had talked to the Queen before the birth.
Since she was a small child, the Queen’s nickname among her family members has been Lilibet.
Some have viewed the move as the couple’s attempt to ‘reach out’ to Harry’s family following months of upheaval.
But, in yet another twist in the drama, Omid Scobie, a close friend of the Sussexes, slammed the BBC report an hour later, insisting that the Queen was the first person Harry contacted after his daughter was born.
Mr Scobie further stated that if the Queen had not approved of the name Lilibet, the pair would not have chosen it.
The spokesman for Prince Harry and Meghan Markle said: “The Duke spoke with his family in advance of the announcement, in fact his grandmother was the first family member he called.
“During that conversation, he shared their hope of naming their daughter Lilibet in her honor.
“Had she not been supportive, they would not have used the name.”
“Those close to Prince Harry confirm that he spoke to close family before the announcement so perhaps this report highlights just how far removed aides within the institution, who learned of the baby news alongside the rest of the world, are now from the Sussexes’ private matters,” tweeted Scobie, who is considered a friend of the couple.
In recent months, the couple’s relationship with the Royal Family has made headlines.
In an explosive interview with Oprah Winfrey earlier this year, while the couple was expecting their daughter, they voiced concerns of the Royal Family and made a racist claim.
Despite the issues between him and his father, Harry stated that he and the Queen had a “really good” relationship and that they chatted through video chat on a regular basis.
The Duke and Duchess of Sussex welcomed their baby on Friday morning before announcing her birth on Sunday, and she was named Lilibet Diana Mountbatten-Windsor, which made headlines.
When the 95-year-old Queen was too young to pronounce her own name, she devised the term ‘Lilibet.’ Her grandfather, George V, was the first to use it, and her husband, Prince Philip, used it until he died earlier this year.
As the Sussexes strive to mend the wounds they have made in their attacks on the Royals, some pundits have speculated Lili’s name was supposed to be an “olive branch”
However, if they use such a particular pet name – which is only used by the Queen’s father, King George VI, and a few close friends – without asking permission, it may be interpreted as an insult rather than a tribute.
Lilibet is the Queen’s 11th great-grandchild and the second child of the Duke and Duchess of Sussex. She is the eighth in the line of succession to the throne.