Knox Grammar School was advised to destroy documents relating to child sexual abuse while at the same time preparing an apology to victims, a royal commission has heard.

A series of emails tendered in evidence to the Royal Commission into Institutional Responses to Child Sexual Abuse revealed an unnamed solicitor had recommended the destruction of documents in 2009, following the arrests of five teachers who abused children at the Uniting Church school.

In one email with the subject heading: "apology drafts", implicates former moderator of the Uniting Church in Australia, Synod of NSW and the ACT, James Mein in the act.

"The solicitor who drafted this is one who has been advising the school to destroy documents, with Jim's assistance," Uniting Church manager of insurance and property services Dwane Freehely wrote.

Rob Wannan, a high profile solicitor and chairman of the Knox Grammar School Council from 2007-13, said the "Jim" in the email was likely to be Mr Mein but denied that he, Mr Wannan, ordered the destruction of the documents.

James Mein has been called to give evidence to the commission.

The current head master of the Wahroonga school John Weeks said he did not believe members of the school council or Mr Mein would destroy evidence.

"It is unconscionable that they would," he said.

He told the commission he wished the files could be found because that "could have saved . . . considerable angst."

The commission has previously heard evidence that a number of student and staff files are missing or incomplete.

Mr Weeks told the commission he first heard rumours about the inappropriate behaviour of one teacher, Adrian John Nisbett, in the mid-1990s.

Nisbett started working at the school in 1971 and the commission has heard he abused a number of students over a 30-year period.

Mr Weeks told the commission he believed former head master Ian Paterson was covering for Nisbett.

"Adrian Nisbett was considered to be a protected species at Knox Grammar School . . . protected by the head master," he said.

When Mr Weeks became head master in 2004 he told the commission he wanted to sack Nisbett, then the head of student welfare, on the spot.

"There were red flags everywhere from my point of view . . . I wanted him gone," he said.

Nisbett was allowed to "resign" in September 2004 following an internal investigation by the school which was given to the NSW Ombudsman but not sent to the police.

Former Knox general duties master Stuart Pearson told the commission that Dr Paterson was "in denial" about the sexual abuse of students. Mr Pearson investigated the behaviour of Nisbett, Craig Treloar and Christopher Fotis and provided reports to Dr Paterson.

"He was reluctant to accept the information that I had provided to him," he said. "In some cases there was just straight out denial."

Nisbett was arrested in 2009 and convicted of a number of sex offences involving three students. The commission heard he is in South Africa and is unable to be summonsed.

A warrant for the arrest of Christopher Fotis remains in place. Dr Paterson is expected to give evidence early next week.

The hearing before Justice Jennifer Coate continues.

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