The Sunday Telegraph has learnt that the first draft of Jonathan Dimbleby's authorised biography of the prince detailed how Diana became "too close" to Mr Mannakee. Royal sources say that Mr Dimbleby obtained the information for his book, The Prince of Wales, because Charles sanctioned that long-serving staff, including other protection officers who knew of the affair, could be interviewed by the author and broadcaster.
Yet it was the prince who, after reading the first draft, persuaded Dimbleby to remove passages relating to the affair.
It is understood the request was made on the grounds of "taste" and because Charles did not want to distress his sons.
According to senior sources, he did not dispute the accuracy of what Mr Dimbleby had written: the heir to the throne had learnt about his wife's affair in 1986, eight years before the Dimbleby book was published.
The attempts by staff to "out" the affair were, however, only temporarily thwarted. It was eventually disclosed by Penny Junor in her "unauthorised" book Charles: Victim or Villain? published in 1998, a year after Diana's death