Extracts from correspondence between Charles and the clergyman before the latter was jailed in 2015, which have been read to the Independent Inquiry into Child Sexual Abuse, reveal the prince sympathised with Ball after he had received a caution in 1993.
Ball, now aged 86, was too unwell to give live evidence, the inquiry heard, but he submitted a lengthy statement.
He said he had "good reasons" for wanting the letters, which he said he handed over to the Lambeth Palace library a number of years ago, to remain confidential, but did not give any detail as to what they were.
He said: "When I did so I expressed the wish that they were to remain confidential and unavailable for viewing until after the death of Prince William and Prince Harry (without going into the specific reasons why, they were good reasons)."
The now-disgraced bishop said he got to know Charles better after his divorce from Diana, Princess of Wales, and said he had known the family of the now Duchess of Cornwall.
In his witness statement, he said of Charles: "Our relationship was one of support and respect. I would strongly resist any suggestion that in some way I could bring pressure to bear on him to act on my behalf and have certainly never made a request for him to do so."
He added: "I considered HRH to be a basically good man and a man with a faith which we would share and which I would encourage him in."
In a letter to the inquiry read on Friday, Charles said he had not been aware of the nature of the complaint which led to Ball's 1993 caution, and that he regretted being "deceived" by the bishop over many years.
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