The latest letter emerged as the Vatican battles a series of allegations that Benedict blocked investigations and disciplinary procedures against priests suspected of sex abuse when he was a senior Vatican official.
In the letter, Benedict raised concerns over what the defrocking of Reverend Stephen Kiesle, a California priest convicted in 1978 of tying up and molesting two young boys in San Francisco, could "provoke with the community of Christ's faithful, particularly regarding the young age of the petitioner".
After his conviction Kiesle asked to leave the priesthood and the diocese submitted papers to Rome to begin the process of defrocking him.
John Cummins, then a bishop in the US, wrote to the Vatican arguing that Kiesle should be stripped of his priesthood.
"It is my conviction that there would be no scandal if this petition were granted and that as a matter of fact, given the nature of the case, there might be greater scandal to the community if Father Kiesle were allowed to return to the active ministry,'' he wrote.
But in the letter Cardinal Ratzinger says that Kiesle should be provided with "as much paternal care as possible" while awaiting a final decision.
Kiesle remained a priest until 1987. He was convicted of more sex offences against children during the 1990s and now lives as registered sex offender in California.
The new allegations come on the heels of a series of child-sex scandals involving the Catholic Church.
Last month, a story in the New York Times newspaper published internal church documents regarding a paedophile priest in the USA.
The Reverend Lawrence Murphy was accused of abusing up to 200 deaf boys from the 1950s to the 1970s.
Among documents the New York Times posted on its website was a 1996 letter about Murphy to Benedict, then the Vatican's senior doctrinal official, showing he had been informed of the case.
Benedict's deputy first advised a secret disciplinary trial but dropped the plan in 1998 after Murphy appealed directly to him for clemency. Murphy died later that year.
The Vatican has reacted defiantly to the suggestion that Benedict had been involved in a cover-up of Murphy's paedophilia, dismissing the allegations as "petty gossip".
Before the latest letter surfaced on Friday, Benedict expressed a willingness to hold new meetings with victims of sexual abuse by Catholic priests.
The Vatican also said that the Catholic Church should work with local law-enforcement authorities to tackle the problem of paedophile priests and "regain trust" lost in the scandal.