Mr Al-Fayed erected the shrine at the base of the shop's Egyptian Escalator soon after the couple's deaths.
Called Innocent Victims, it shows the pair with their hands raised towards a seagull.
The statue of Diana, Princess of Wales and Dodi Al Fayed was unveiled at Harrods on September 1, 2005.
The surprise was not that it is going, but that it lasted this long. "I always thought it was tacky".
Al Fayed commissioned the bronze statue, which shows his son and Diana, after they were killed in a Paris vehicle crash in 1997.
Camera IconCrowds outside Harrods in 1997 where pictures of Diana and Dodi were placed in a window.
For eight years the permanent memorial that Mohammed Al Fayed created to his son Dodi and Diana, Princess of Wales, has remained at Harrods, despite his sale of the store to the Qatari royal family in 2010.
The iconic Knightsbridge department store, long a symbol of great opulence and extravagance, had enjoyed unrivalled financial success but since 2000 had lacked the one thing to which ambitious retailers aspire: a royal warrant.
The statue was installed at Harrods in 2005
The first part of the memorial featured photos of the lovers.
But the store's managing director, Michael Ward, said it was now time to return it, noting that Diana's sons Princes William and Harry were commissioning their own statue to their mother at Kensington Palace.
Store bosses said they had consulted Mr Fayed on the move but would not say how he felt.
Royals stopped shopping at the popular central London site after Fayed accused the Duke of Edinburgh of ordering the murders of his son and Diana by staging the 1997 Paris vehicle crash which resulted in their deaths.
The Al Fayed family said in a statement: "We are grateful to Qatar Holdings for preserving the Dodi and Diana memorial at Harrods until now. It is now time to bring them home".
This story originally appeared in The Sun and was republished with permission.
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