The Duke and Duchess of Sussex made several allegations in the bombshell TV interview, including that there were 'conversations and concerns' about what colour their then unborn child would have.
They also accused the Palace machinery of failing to support Meghan when she had 'suicidal' thoughts.
The Queen waited more than two days before releasing a short statement which said that, 'while some recollections may vary', the 'whole family' was 'saddened' to hear of the couple's 'challenging few years'.
Now, royal biographer Robert Jobson has said that, while the palace statement was in the Queen's words, the Prince of Wales is likely to have 'taken the lead' on the response.
He said the Royal Family like to 'do things as a team' and to react 'as a family' when being criticised.
Prince Charles 'took the lead' on Buckingham Palace's response to Prince Harry and Meghan Markle's interview with Oprah Winfrey, a royal expert has claimed
Writing for Hello! magazine, he said: 'I think the Prince of Wales has also taken the lead on how the Palace has responded,' the Mirror reported.
'The Queen is 94 and the Duke of Edinburgh is incapacitated, so he will be trying to placate and learn lessons from this so something can be worked out to everyone's satisfaction.'
He added: 'The royal family like to do things as a team, and if the team is being trashed they like to react as a unit and a family.'
Jobson also praised the Queen's response, describing it as 'dignified'.
Along with Charles, the monarch was reportedly set to speak with the Duchess of Cornwall as well as Prince William and his wife Kate about Harry and Meghan's allegations.
On Thursday, the Queen was said to be 'sad but not angry' about the interview.
The Duke and Duchess of Sussex made several allegations in the bombshell TV interview, including that there were 'conversations and concerns' about what skin colour their unborn child would have
The Queen waited more than two days before releasing a short statement which said that, 'while some recollections may vary', the 'whole family' was 'saddened' to hear of the couple's 'challenging few years'
The skin colour allegation sparked a frenzy with royal watchers speculating about the identity of the family member who made the comment.
But sources said the Queen was not angered by the interview and instead has privately pledged to stand by Harry.
An insider told the Sun: 'She is not angry, she is just sad. They have always worried about him (Harry) and the Queen feels very protective about him.
'They always tried to support him when Meghan came along. They all worried less about him when Meghan was on the scene as he seemed so happy.'
Prince William later said the royals are 'not a racist family' with the Queen ordering a private family investigation into the claims.
American broadcaster Gayle King revealed on US TV last week that William had taken part in an 'unproductive phone call with Prince Harry'.
The revelation - which the CBS presenter delivered live on air - has reportedly made William wary of engaging further with the couple, fearing that any talks with his brother will be leaked to American television networks.
Sources told Vanity Fair there was concern within the family that the Sussexes 'want to keep fuelling the soap opera'.
The bombshell revelations from Harry and Meghan's interview with Oprah Winfrey
During the couple's tell-all (pictured), Meghan addressed reports that she made her sister-in-law cry over a disagreement regarding bridesmaid dresses ahead of the royal wedding, while the couple also revealed they were having a baby girl
- Meghan's mental health
The Duchess of Sussex revealed she had suicidal thoughts and said: 'I just didn't want to be alive any more.'
She said she begged for help, and asked to go somewhere to get help, and approached one of the most senior people in the institution, but was told it would not look good.
The duchess said: 'I said that I needed to go somewhere to get help. I said that I've never felt this way before and I need to go somewhere. And I was told that I couldn't, that it wouldn't be good for the institution.'
- Baby Sussex is a girl
Harry and Meghan revealed they are expecting a baby girl. The duke joined his wife in the second half of the interview, and told the chat show host: 'It's a girl.'
He said his first thought was 'amazing' when he discovered they were having a girl, adding: 'Just grateful. To have any child, any one or any two, would have been amazing.
'But to have a boy and then a girl, I mean what more can you ask for? Now we've got our family, we got the four of us and our two dogs.'
Asked if they were 'done' with two children, Harry said 'done' and Meghan said: 'Two is it.'
She also confirmed the baby is due in the 'summertime'.
- Royal family accused of racism
Meghan said, when she was pregnant with Archie, an unnamed member of the royal family raised 'concerns and conversations about how dark his skin might be when he's born'.
Asked whether there were concerns that her child would be 'too brown' and that would be a problem, Meghan said: 'If that is the assumption you are making, that is a pretty safe one.'
Pushed by Winfrey on who had those conversations, Meghan refused to say, adding: 'I think that would be very damaging to them.'
She added: 'That was relayed to me from Harry, those were conversations the family had with him, and I think it was really hard to be able to see those as compartmentalised conversations.'
- Archie's title
Meghan suggested she and Harry wanted Archie to be a prince so he would have security and be protected.
The duchess expressed her shock at 'the idea of our son not being safe', and the idea of the first member of colour in this family, not being titled in the same way as other grandchildren.
Archie, who is seventh in line to the throne, is not entitled to be an HRH or a prince due to rules set out more than 100 years ago by King George V.
He will be entitled to be an HRH or a prince when the Prince of Wales accedes to the throne.
As the first born son of a duke, Archie could have become Earl of Dumbarton - one of Harry's subsidiary titles - or have been Lord Archie Mountbatten-Windsor, instead at the time of his birth, a royal source said Harry and Meghan had decided he should a regular Master Archie Mountbatten-Windsor.
- The Prince of Wales
The Duke of Sussex said his father the Prince of Wales stopped taking his calls while Harry and Meghan were in Canada 'because I took matters into my own hands. I needed to do this for my family'. He said Charles wanted him to put his plans in writing.
- The Queen
Harry denied that he had 'blindsided' his grandmother Queen with the bombshell statement about stepping down as senior royal.
The duke said he believed the report probably could have come from 'within the institution'.
- The Duchess of Cambridge
Meghan said Kate made her cry ahead of her wedding. Reports circulated ahead of the Sussexes' nuptials that Meghan left Kate in tears at Princess Charlotte's bridesmaid dress fitting.
But Meghan told Winfrey the 'reverse happened'.
Meghan said she was not sharing the information to be 'disparaging', but added it was 'really important for people to understand the truth'.
'She's a good person,' the duchess added.