A defensive Cardinal George Pell gave evidence to the royal commission into institutional responses to child sexual abuse on Monday, claiming ignorance of key aspects of the infamous John Ellis case and rebuffing much of the testimony given by church representatives in previous days.

Pell, appearing at the public hearing before taking up a senior role at the Vatican next Monday, described one former colleague as "a muddler" who was "sometimes illogical".

The hearing is examining the Catholic church's response to allegations made by the former altar boy John Ellis, who was abused by his parish priest, Father Aiden Duggan, in Sydney between 1974 and 1979. Ellis sued the church in 2007 but lost when the supreme court ruled that the church an entity could not be sued.

Senior counsel assisting the commission Gail Furness first took Pell through the minutes of several meetings of the Australian Catholic Bishops Conference in the 1990s which discussed the development of the church’s Towards Healing process and other responses to claims of child sexual abuse by clergy.

Pell spoke highly of the Australian bishops' efforts to address abuse claims, and said that by 1996 Australia was "ahead of some countries”. The Australian bishops had spoken with other churches around the world but he did not know what conversations had been had with the Holy See.

"The attitude of some people in the Vatican," said Pell, was that claims of child abuse were "accusation by enemies of the church to make trouble … and should be taken sceptically," with the "benefit of the doubt [given] to the defendant".

Pell told the commission a group of church representatives later lobbied the Vatican and explained that complaints were not always by "enemies of the church for political purposes" as Nazis and Communists had been, he said.

Furness drew applause when she called for specific data after Pell claimed statistics from a number of uncited studies to support the notion that the number of abuse claims could be exaggerated.

Her questioning also established that the Melbourne Response had been set up quickly under Pell's new leadership of that diocese, despite the national Towards Healing process being well under way. Because the Melbourne Response was launched five weeks before Towards Healing, it was not subject to the national processes. When Pell moved to Sydney he then worked with Towards Healing – about which he told the commission he had reservations – including on the Ellis case.

Pell has maintained he was not aware of aspects of the case, including the amount Ellis was seeking for compensation. In an excerpt from his statement read out on the first day of the hearing, Pell said he had thought Ellis was asking for millions of dollars, not $100,000.

On Monday he told the hearing he "could not recall ever being asked my opinion on how much money might be paid for reparation compensation to a Towards Healing victim".

Previous witnesses have suggested Pell was in fact involved in key decisions, including the ferocity with which the church's lawyers defended the case, and the response to any amount being sought by Ellis.

A former vicar general and chancellor of the Sydney Catholic archdiocese, Monsignor Brian Rayner, told the commission that he had spoken with Pell about "every amount of money that was being offered to any particular victim" and, though he had seen Pell's statements to the contrary, he believed Pell's recollection of events was "not clearly accurate".

On Monday Pell told the commission Rayner was wrong. "I certainly did not participate in any extended discussion on this matter … or nominate any amount of money. There are a whole lot of things wrong with [Rayner’s] account," he said.

Pell also disputed the testimony given by his former private secretary Michael Casey, who said all significant matters, including those about child sexual assault, had been put to Pell.

The cardinal said that statement was "incomplete". "Sometimes these matters were discussed with me … and on many occasions they weren't, because I'm not a micromanager," he said.

"It's impossible. My practice was to give people a job and let them get on with it. Until they established that they were mucking things up, that's exactly what I did."

He said he was not regularly informed of particular amounts.

Pell earlier told the hearing that when any accusation of child sexual abuse by clergy came in he would see it immediately referred to the office of professional standards – the church's committee to deal with child abuse – which then took full responsibility. But a number of mistakes were made in the handling of Ellis's case.

Under questioning, Pell described the former director of professional standards, John Davoren, as "a muddler" who sometimes "wasn't logical".

"He didn't seem to have a scrupulous understanding or commitment to following protocols," Pell said.

One of these protocols was for Davoren to appoint an assessor of Ellis's claim, independent of himself, the commission heard.

This was not done by the time a letter was sent to Ellis which read "it is now clear the facts of this case can never be satisfactorily clarified" – because Duggan was suffering dementia and could not be questioned.

Pell conceded that in the light of present information that sentence was plainly wrong, but he did not know it to be wrong at the time. He took responsibility for significant changes made to a draft letter written by Davoren for Pell to send to Ellis, including the removal of key phrases expressing regret or responsibility.

Pell removed the phrase "it's not to say you are disbelieved" from the letter before it was sent to Ellis. "I wasn't going to say in effect that we believe Mr Ellis,” Pell said, “when the point of Mr Davoren's advice was that this couldn't be established.”

Commissioner Peter McClellan put to Pell that the letter Ellis had received was "a rejection", a point Pell conceded but said he was following advice from the professional standards office.

"I regret what I did,” he said. “It was a mistake. To say that something could not be satisfactorily established is one form of rejection. It's not a denial that something took place.

"I didn't want to be saying contradictory things. I didn't want him to be feeling that something was going to be done that wasn't going to be done. I didn't want to mislead him."

Furness asked Pell if he meant it was misleading to suggest "that anything was going to be done for him".

"Yes, yes. If it couldn't be done towards clarifying – if we couldn't clarify the situation, I didn't want to suggest that we were," Pell replied.

He also removed a passage which read "I very much regret any hurt that you have experienced", because it was "quite illogical" he told the hearing. "Because if hurt had been caused, that would indicate that the case was believed, that the case was established," he said.

"I didn't think that the letter could have it both ways. If the case couldn't be established, then the hurt couldn't be established. That was my reasoning. I was attempting to be honest."

Ellis previously told the hearing that receiving that letter was like having a door slammed in his face.

The hearing continues.