County Court judge Roy Punshon said he had come to a pragmatic decision to allow Cardinal Pell limited access.

Lawyers for Cardinal Pell had applied to the court for access to the transcript of the trial involving Best and one of his victims so he could have the information before he was expected to be called before the Victorian parliamentary inquiry investigating how churches dealt with sex abuse.

The victim, known as V2, claims Cardinal Pell was present when the boy told another priest he had been 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, 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 the Victorian parliamentary inquiry,

Judge Punshon said Best had been involved in a series of trials, including the one involving V2 where a jury had found the priest guilty in December 2010 of one count of buggery.

The judge said V2 had alleged during Best's trial that he had asked to speak to Cardinal Pell at the presbytery at St Alipius Primary School in Ballarat.

Cardinal Pell allegedly refused to speak to him.

V2 claimed Cardinal Pell was later present when the boy described to another priest what had happened to him.

Judge Punshon said Cardinal Pell denied being in Australia in 1969 and believed what was being alleged against him was unclear, so the best source of finding out would be in the trial transcript.

The problem the judge had was that sensitivity was required because Best's trial involved sexual allegations.

The judge had looked at the trial transcript and he did not believe editing out V2's name would protect his identity as there were still details of his personal characteristics and his background.

Judge Punshon said he also had concerns that the intimate features of the case would be disclosed in the transcript.

He believed the best solution was to grant access to certain important passages of the transcript that did not require editing.

The passages included V2's evidence about when he made the complaint about Best to the priest in the presbytery, and details of his meetings with priests.

There were also extracts from Best's evidence where he discussed the identity of the priest V2 had confided in.

Judge Punshon said the defence made the point during Best's trial that the identity of the priest V2 had confided in and who else was present at the time had always been an issue at trial.

The judge said he had tried to be as careful as he could with the passages to be released to protect V2's identity.

"It's a matter for the parties what they want to do with that material," he said.

Both Cardinal Pell and Dr Waller have yet to hear if and when they will have to attend the Victorian parliamentary inquiry.

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.