Three weeks earlier, Cardinal Pell had received a report from an independent investigation by Howard Murray into Father Goodall. This advised him that the complaints of both men should be upheld, but Cardinal Pell's letter to Mr Jones directly contradicted that advice. Cardinal Pell did not respond last night. But Mr Jones told the Herald he believed Cardinal Pell should resign. "The apology that the Pope may give [to church abuse victims] has no meaning if the Archbishop of Sydney is still covering up sexual assaults," he said. "[Pell] assaulted me all over again through his lies. I had to live through these two sexual assaults through his lies."

Mr Jones, now a 54-year-old disability pensioner, was 29 and training as a teacher when Father Goodall assaulted him in a Sydney pool - and then again that night in a presbytery - in 1982. Cardinal Pell, in his letter to the other victim, acknowledged that Father Goodall had also engaged in "inappropriate behaviour" with altar boys. In 2005, Father Goodall pleaded guilty to two counts of indecently assaulting Mr Jones. He had also been charged with attempted buggery, but pleaded guilty only to indecent assault. He was sentenced under old laws which, at the time of the encounter, had banned even consensual sexual contact between men. The case was controversial for its retrospective use of the laws - and Father Goodall was given a token sentence of four seconds.

Mr Jones first complained to the church in the days after the assault. In 2002, he complained again, as did the other victim. The report into their complaints was delivered to Cardinal Pell a month before he wrote to the victims in 2003. Contrary to Cardinal Pell's claim to Mr Jones, the report did not indicate that Father Goodall "categorically denies the accusation". Nor did it recommend the two victims be dealt with in a different manner.

"Given the admission volunteered by Fr Goodall, it can be concluded that the allegations made by Tony and [Boy X] are sustained," Mr Murray, the independent assessor, wrote. He recommended "both Tony and [Boy X] be informed in writing that their allegations have been sustained". He found "Fr Goodall readily admitted to the behaviour complained of by Tony … He agreed that he had fondled Tony's penis without consent in the pool as a result of 'a physical attraction'." According to the report, Father Goodall agreed generally with Mr Jones's account of the events that then took place on a bed, although said it was "more consensual, than forced upon Tony". "He cannot recall whether he ejaculated, as alleged by Tony, but agreed it was likely," the report found.

In his letter to the other victim, Cardinal Pell accepted that he had been attacked by Father Goodall. "After examining all the material, Mr Murray provided me with a report in which he recommended that the complaints of inappropriate behaviour with altar boys and of indecent assault of you when a young boy be found to be substantiated." Mr Jones said the second victim validated his case beyond the technical issue of homosexuality.

The victims' support group Broken Rites called for Cardinal Pell to stand aside while the matter was investigated. Despite repeated requests, the Herald had received no response from Cardinal Pell at the time of publication. But early this morning Cardinal Pell issued a statement denying there was a cover-up or that he tried to mislead Mr Jones. "There was no attempt at a cover-up," he said. "The letter to Mr Jones was badly worded and a mistake - an attempt to inform him there was no other allegation of rape."

"However, I signed both letters of February 2003 mentioned in the ABC's Lateline program, and any fault in the drafting was mine. "The accusations against Father Goodall were investigated by the church and the police and Father Goodall was stood down.

"In a subsequent letter soon after the February 2003 letter I expressed my sorrow at what Mr Jones had suffered and offered to meet him. "There was no attempt to mislead him. I apologise for the confusion caused to Mr Jones."