A spokesman for the Prince of Wales said Bortrick has never worked for the prince.
The spokesman added: "The Prince of Wales has no knowledge of the alleged offer of honours or British citizenship on the basis of donation to the charities and fully supports the investigation now underway by The Prince's Foundation."
According to The Times, in a draft letter to Mahfouz, Bortrick who is the publisher of Burke's Peerage, said the application for citizenship would "now take the highest priority".
He added: "His Royal Highness supports these applications one hundred percent, as there is no greater example of contribution [than] yours, therefore this should be rewarded and recognised accordingly."
He claimed Mahfouz would meet the Queen "in the next few months".
And said Mahfouz would be given the "special honours" of a knighthood followed by full membership of the House of Lords.
There is no evidence, however, of whether the letter, drafted in May 2014, was sent or agreed by Charles's advisers.
Fawcett temporarily stepped down as chief executive of the Prince's Foundation.
Charles was with the Duchess of Cornwall and had face to face meetings with Prime Minister Boris Johnson and wife Carrie at his home on the Queen's Balmoral estate on Sunday.