"I regret that one of my first duties as Bishop is to continue Canonical procedures against one of the priests of the Diocese," the document, dated November 2, 1995, said.
"Because of the gravity of the allegations against you, the evidence supporting those allegations, and after full and continual consultation with Bishop [Leo] Clarke over many months, I have no alternative but to reaffirm the contents of Bishop Clarke's letter to you of October 19," the document said.
It confirmed that Bishop Clarke's "speedy resolution" time frame of seven weeks "still stands".
"In conclusion may I emphasise the seriousness of the allegations and the real possibility of police intervention," the document ended.
Bishop Malone refused last week to comment on whether the Vatican was petitioned about McAlinden.
McAlinden's movements are not known between October 1995 and 1999, when the Maitland Newcastle diocese advised the church's Professional Standards Resource Group that McAlinden was "in England celebrating his Golden Jubilee" as a priest, noting he was doing so "despite the fact that his facilities have been removed since 1993", so he was acting as a priest without church approval.
"We suspect that he will come back to Australia late in August and reside somewhere in the Bunbury region of Western Australia," the diocese's letter noted.
The church paid compensation to two of his victims in 2001 and 2002, and further payments to other victims last year.
McAlinden died in a St John of God villa in Western Australia in November 2005.
In October 2007, after a series of articles in The Herald, the Catholic Church was forced to confirm that the Irish-born McAlinden, who arrived in Australia in 1949, aged 26, to work as a priest in the Maitland Newcastle diocese, was a serial sexual predator of children over many years.
In those articles, Archbishop Philip Wilson confirmed he handled complaints against McAlinden in 1985 and 1995.
In a statement at the time he said he was diocese secretary when he spoke to a woman at Merriwa in 1985 who believed her daughter had been abused by McAlinden.
He said he "asked her to report her concerns to the police, but she decided not to do so".
"I reported this outcome to the Bishop [Leo Clarke]," Archbishop Wilson said.
In response to The Herald's investigations Bishop Malone in October 2007 issued a statement acknowledging "all victims of abuse by church personnel, including those of Father Denis McAlinden".
"The distress and lifelong impact of Father McAlinden's actions on all those affected has not been publicly acknowledged until now," Bishop Malone wrote.
Bishop Malone declined to comment last week on his role in the attempted secret defrocking of McAlinden.
"I will not comment on issues pertaining to deceased members of the diocese" who did not have a "right of reply".
"I am on record with your paper and others saying that I could have handled earlier matters of historical sexual assault better," he said.
"Mistakes were made but we have moved forward."SIC: THCAU