The letter has been released following a Freedom of Information Act request, submitted to the Crown Prosecution Service.
The then Archbisop, Lord Carey, (pictured left) said in the letter that Peter Ball was in "torment" because of the investigation, according to the BBC.
The Church of England (CofE) has apologised "unreservedly" to Ball's alleged victims in response to the letter.
In October Peter Ball, 83, (pictured right) was jailed for a string of historic offences, including two counts of indecent assault.
During his time as the Bishop of Lewes, he chose 18 victims to commit acts of "debasement" in the name of religion, such as praying naked at the altar and encouraging them to submit to beatings.
In 1993 one of the letters written by Lord Carey, he said it was "improbable" that Ball was guilty of the allegations made against him, according to the BBC.
Speaking after Ball's sentencing in October 2015, Lord Carey denied that the Church of England had been involved in protecting him: "I greatly regret the fact that, during my tenure as Archbishop of Canterbury, we dealt inadequately with Peter Ball's victims and gave too much credence to his protestations.
"Allegations by some that my actions amounted to a cover-up or collusion with the abuser are wrong. I have always insisted upon the highest standards of holiness of life from all who are ordained."
A CoE in response to the letters said that: "It is a matter of deep shame and regret that a bishop in the Church of England was sentenced earlier this year for a series of offences over 15 years against 18 young men known to him.
"There are no excuses whatsoever for what took place, nor for the systematic abuse of trust perpetrated by Peter Ball.
"We apologise unreservedly to those survivors of Peter Ball's abuse and pay tribute to their bravery in coming forward.
"They have had to endure a long wait for justice over decades. We also remember Neil Todd, whose bravery in 1992 enabled others to come forward but who took his own life before Peter Ball's conviction or sentencing."
It added that Ball had "systematically abused the trust of the victims" and abused the trust placed in him by the church and others, "maintaining a campaign of innocence for decades until his final guilty plea earlier this year".
Lawyer David Greenwood, who represented victims of Ball, said this seemed as if there had been a case of "parts of the establishment trying to help another part of the establishment".
Speaking on BBC Radio 4's Today programme he noted that: "To receive letters such as those will obviously have had some influence on the Crown Prosecution Service at the time and I would suggest contributed to the decision to allow Peter Ball to be cautioned rather than prosecuted in 1993."
He added that his clients had a sense of a "weight being lifted" but did feel "angry" that Ball "escaped justice" until 2012.
