"We understand their desire to take a different approach, but these are complicated issues that will take time to work through."
In the following days she summoned Harry, Charles and William to Sandringham for a crisis summit to work out what was going to happen next.
She chaired the meeting, in which the family worked out six points that needed to be sorted before progress was made.
After the discussions were over, the Queen released another statement on the issue in which she referred to the couple as Meghan and Harry rather than using their HRH titles.
She said: "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.
"Harry and Meghan have made clear that they do not want to be reliant on public funds in their new lives.
"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."
Meghan Markle and Prince Harry's decision to quit their roles as senior members of the Royal Family reportedly left the Queen extremely upset.
According to insiders the couple didn't consult their relatives before making the life-changing decision, causing a lot of anger behind Palace walls.
Harry's grandmother the Queen has released two official statements on the controversial issue, saying that while she is disappointed by their decision she understands their desire for a more private life.
After Meghan and Harry's initial announcement, which they posted on Instagram rather than through official channels, the Queen released a short but firm statement.
It said: "Discussions with The Duke and Duchess of Sussex are at an early stage.