It was reported that Meghan didn't dial into the meeting via conference call from Canada because palace officials working for Her Majesty, Charles and William feared the talks could have been recorded or intercepted.
Read more: Queen releases statement on Harry and Meghan
However, the couple's Kensington Palace spokesman denied the claims Meghan had been shut out from the meeting.
A statement said: "In the end, the Sussexes decided that it wasn't necessary for the Duchess to join."
Meanwhile, it's been said that the Duke of Sussex arrived two hours early for the meeting because he wanted to secure a one-on-one chat with his grandmother to put across his side of the story.
On Monday evening, a statement from the Queen said she has "asked for final decisions to be reached in the coming days".
The statement read: "Today my family had very constructive discussions on the future of my grandson and his family.
"My family and I are entirely supportive of Harry and Meghan's desire to create a new life as a young family.
"Although we would have preferred them to remain full-time working Members of the Royal Family, we respect and understand their wish to live a more independent life as a family while remaining a valued part of my family."
In the end, the Sussexes decided that it wasn't necessary for the Duchess to join.
The statement said that Meghan and Harry have "made clear that they do not want to be reliant on public funds in their new lives".
The Queen added: "It has therefore been agreed that there will be a period of transition in which the Sussexes will spend time in Canada and the UK.
"These are complex matters for my family to resolve, and there is some more work to be done, but I have asked for final decisions to be reached in the coming days."
It comes after the Duke of Cambridge and Duke of Sussex issued a statement yesterday to deny reports Harry was feeling forced out of the royal family because of his brother's "bullying attitude" towards he and Meghan.
A spokesperson for the pair said: "Despite clear denials, a false story ran in a UK newspaper today speculating about the relationship between The Duke of Sussex and The Duke of Cambridge.
"For brothers who care so deeply about the issues surrounding mental health, the use of inflammatory language in this way is offensive and potentially harmful."
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