A judge said he had "a sense of anxiety or discomfort" about a request by Cardinal George Pell for sensitive material relating to the trial of convicted paedophile and Catholic brother Robert Charles Best.
But County Court judge Roy Punshon said he recognised some of the material sought by Cardinal Pell was highly relevant to the allegations made against him.
Lawyers for Cardinal Pell have applied to the County Court for access to the transcript of the trial involving Best and one of his victims.
The victim, known as V2, claims Cardinal Pell was present when the boy had complained of being raped by Best.
Cardinal Pell has described the victim's claims as "irresponsible, untrue" and said they were "absolutely denied".
The Archbishop of Sydney has said he was not in Ballarat in 1969 when the boy was raped and had not been appointed to the diocese until 1973.
It is also understood that the victim, during his evidence at the trial, did not raise the allegation about Cardinal Pell being present, and said that he was unsure who had been there.
The allegation was made last month by lawyer Vivian Waller, who acts for more than 70 victims of abuse by Christian Brothers. It was included in Dr Waller's submission to a Victorian parliamentary inquiry investigating how churches dealt with sex abuse.
Lawyer Timothy Seccull, representing V2, told the court today his client opposed Cardinal Pell's application for access to the trial transcript.
Mr Seccull said both the purpose of the application and its intended use must be clear.
He said it should not be a case of Cardinal Pell stepping into the shoes of the parliamentary inquiry to seek access to the material.
Any application for the transcript ought to be made by the inquiry or ultimately the royal commission into child sex abuse, not Cardinal Pell, Mr Seccull said.
Lawyer Marcus Hoyne, representing Cardinal Pell, said there was a submission before the parliamentary inquiry that his client "did various things".
Mr Hoyne said Cardinal Pell was simply being pro-active in making the application and wanted the information made available before he was expected to be called to give evidence at the inquiry.
He did not want to wait for the inquiry's findings to be handed down.
Mr Hoyne did not know if Cardinal Pell knew who V2 was but his client was not concerned if V2's name was removed from the trial transcript before access was granted.
Both Cardinal Pell and Dr Waller have yet to hear if and when they will have to attend the inquiry.
Judge Punshon said he would hand down his decision on Cardinal Pell's application on a date to be fixed.
The judge jailed Best for a minimum of 11 years and three months in August last year for molesting young boys during a 20-year period at three Victorian schools.
The offences related to 11 boys he taught at St Alipius Primary School in Ballarat, St Leo's College in Box Hill and St Joseph's College in Geelong between 1969 and 1988.
The former school principal was found guilty of 21 charges and later pleaded guilty to a further six.
Best lost a Supreme Court appeal on Wednesday against seven convictions for indecently assaulting one schoolboy between 1971 and '74 while principal at St Alipius Primary School.
In his judgment, Justice Robert Osborn said there was no requirement for the complainant's evidence to be corroborated and there was no evidence of a miscarriage of justice.