Mr Markle told celebrity news website TMZ, at his home in Mexico, that he had decided not to attend his daughter's wedding to Prince Harry.
Kensington Palace issued a statement saying it was "a deeply personal moment for Ms Markle".
It follows Mail on Sunday reports that Ms Markle's father had staged pictures for a paparazzi photographer.
The widely circulated photographs showed him being measured for a wedding suit and looking at newspaper stories about his daughter.
He is reported to have said that he didn't want to cause his daughter embarrassment by attending the wedding.
A Kensington Palace spokesman said: "This is a deeply personal moment for Ms Markle in the days before her wedding.
"She and Prince Harry ask again for understanding and respect to be extended to Mr Markle in this difficult situation."
Mr Markle had been due to meet Prince Harry for the first time this week, as well as the Queen and the Duke of Edinburgh, before walking his daughter down the aisle at St George's Chapel in Windsor Castle.
The controversy surrounds pictures of Mr Markle, which were published earlier this month in a number of newspapers showing him in a series of wedding related activities - apparently unaware he was being photographed.
Samantha Markle, Ms Markle's half-sister, has claimed she is to blame for the photographs.
The wedding should come already
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