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The 98-year-old Duke of Edinburgh was said to be furious over the couple's shock announcement, accusing them of disrespecting the Queen.
Philip, who is now largely bed-ridden at Sandringham's Wood Farm, has always been extremely close to Harry. The Sun newspaper reports the Queen's husband has been left "deeply hurt" at the Sussexes' decision to step back from duties.
The shock move to spend a large part of their time n Canada — suddenly revealed on social media — comes just weeks after the Prince was treated in hospital in the run-up to Christmas.
The Sun reported a source as saying, after being briefed by aides over the statement by Harry and Meghan.: "To say that the Duke feels let down would be a considerable understatement. He is deeply hurt."
Notoriously, Philip has not been a fan of Canada in the past, once reportedly commenting: "We don't come to Canada for our health. We can think of other ways of enjoying ourselves."
Earlier, Prince William spoke publicly for the first time about his younger brother's choice to separate from the royal family, saying he hopes that the royals can make amends.
The two brothers will meet with their father and grandmother, Queen Elizabeth II, on Monday at Sandringham estate in hopes of reaching an understanding.
Though Meghan will be staying in Vancouver with eight-month-old Archie, she plans to call in for the meeting.
It will be the first time Prince Harry has seen the Queen and the two direct heirs to the throne since the couple made the announcement.