Prince Harry and Meghan are understood to have disappointed the Queen after failing to consult her about their decision to "step back" from their position as senior royals.
The couple issued a bombshell statement on Wednesday where they also announced their decision to divide their time between the UK and North America.
Despite saying they will "fully support" the Queen, Buckingham Palace was not informed about the statement prior to its release.
Sky's royal correspondent Rhiannon Mills said: "I'm told that the statement was solely written by the Duke and Duchess of Sussex - no senior members of the Royal Family were consulted before it was released."
It is understood Harry and Meghan had just begun talks with the Queen and Charles about their future roles when they made their decision to go public.
The sequence of events has lead some commentators to speculate whether a rift has developed at the heart of the monarchy.
Buckingham Palace warned the couple their decision to step back from the royal family will be "complicated".
In a groundbreaking statement shared on Instagram, the Duke and Duchess of Sussex said: "After many months of reflection and internal discussions, we have chosen to make a transition this year in starting to carve out a progressive new role within this institution.
"We intend to step back as 'senior' members of the Royal Family and work to become financially independent, while continuing to fully support Her Majesty The Queen."
The royals added that they now "plan to balance our time between the United Kingdom and North America, continuing to honour our duty to The Queen, the Commonwealth and our patronages".
Harry and Meghan continued: "This geographic balance will enable us to raise our son with an appreciation for the royal tradition into which he was born, while also providing our family with the space to focus on the next chapter, including the launch of our new charitable entity.
"We look forward to sharing the full details of this exciting next step in due course, as we continue to collaborate with Her Majesty The Queen, The Prince of Wales, The Duke of Cambridge and all relevant parties. Until then, please accept our deepest thanks for your continued support."
Regarding Harry and Meghan's decision, a Buckingham Palace spokeswoman said: "Discussions with The Duke and Duchess of Sussex are at an early stage.
"We understand their desire to take a different approach, but these are complicated issues that will take time to work through."
On Tuesday, the Duke and Duchess of Sussex had resumed their royal duties after taking a family break in Canada.
Crowds, and dozens of photographers, were in Trafalgar Square as Prince Harry and Meghan visited Canada House in Central London to meet Janice Charette, High Commissioner in Canada to the UK and staff.
Following the news, Sky News' royal correspondent Rhiannon Mills said it shows "the pressure that they were under" and that Harry is in a "different phase of his life".
She added that Harry has always had a "difficult relationship with the press since his mother died", and that now he has a wife and son that he wants to protect, it has "changed the dynamic of what he wants to do as a working royal".
Towards the end of last year, both Harry and Meghan admitted they were struggling with the headlines and attention from British tabloid newspapers in a documentary which aired on ITV.
Meghan also revealed her friends told her not to marry Harry, warning her she "shouldn't do it because the British tabloids will destroy your life".
In an interview with ITV's Tom Bradby, Meghan said not many people had asked if she was okay and admitted living in the public eye as a new mother had been a "struggle".
As part of the documentary detailing Prince Harry and Meghan's 10-day tour of Africa, the Duke of Sussex also opened up about his grief following his mother, Diana, Princess of Wales' death.
He said he felt considerable pressure being part of the Royal Family in the spotlight, and every camera flash took him back to his mother's death.
"I think being part of this family, in this role, in this job, every single time I see a camera, every single time I hear a click, every single time I see a flash, it takes me straight back, so in that respect it's the worst reminder of her life, as opposed to the best," he said.
Prince Harry answered a question about rumours of a rift between himself and the Duke of Cambridge, saying he and his brother are "on different paths" and have "good days" and "bad days".
Last year appeared to be a particularly tumultuous time for the royal couple, as they also faced criticism for using private jets over the summer.
Harry responded to the criticism at the launch of an eco-friendly tourism initiative, saying there are occasions he needs to keep his family safe.
"I spend 99% of my life travelling the world by commercial. Occasionally there needs to be an opportunity based on a unique circumstance to ensure that my family are safe," he said, after being asked about his travel.
Shortly after, Harry and Meghan announced that they were suing the Mail on Sunday after a private letter which the couple claim was published in an "intentionally destructive manner" to "manipulate" and to "further the divisive agenda" of the newspaper.
In a strongly worded statement, the duke said his wife had become a victim of the British tabloid press and denounced what he called their "ruthless campaign".
Harry and Meghan's decision comes after a particularly difficult time for the Queen.
Sky's Rhiannon Mills added: "Only at the end of last year we had Prince Andrew stepping back from public duties. It does feel like the Royal Family are in turmoil at the moment, and this is not helpful."
Harry married Meghan, a former actress who starred on the hit TV show Suits, in May 2018 and the couple welcomed their son, Archie, in May last year.