The minutes reveal the money spent representing Herft, one of the most senior figures within the Anglican church in Australia, was not authorised through usual church processes. It came from the diocese's professional standards budget, but without a written resolution authorised by the diocesan council, which expenditure from this budget requires.

The minutes of the following year's meeting show church officials were asked: "Has Bishop Roger Herft been asked to repay any funds used for legal expenses for his appearance before the royal commission?" The answer was "No". That the question was put indicates discontent within the clergy over the legal fees. Herft was a member of the diocesan budgeting group at the time his legal fees were covered.

In a media statement on 30 June 2017, the then diocesan secretary said diocesan leaders "were working on the assumption that most of the legal expenses ... would be recovered through a claim on the Diocese of Newcastle's insurers". This assumption was made without any legal advice, and without advice from insurers.

According to the synod minutes, the $473,707 has since been "reallocated" to the archbishop's establishment fund, which does not require the same authorisation process for spending.

Herft stood aside as archbishop in 2016 after his evidence before the royal commission revealed that while he was the bishop of Newcastle, between May 1993 and February 2005, he failed to report child sexual abuse to police. He accepted that this left children at risk.

A longstanding member of the diocese who was present at annual general meetings of the synod, but who is unwilling to be named in case of repercussions from the leadership, said: "There was no formal approval given by anybody.

"The archbishop also continued to be paid, and for the whole period he was stood aside he lived in Archbishop's House. He was fully paid until he retired. The archbishop receives a package that would have been worth at least $150,000 a year.

"The church as an institution is still protecting Archbishop Roger Herft."

Herft retired in July 2017, one year ahead of schedule, and nine months after standing aside.

The Diocese of Perth did not respond to requests from Guardian-Australia for comment. Attempts to contact Herft were unsuccessful.

On Friday, almost three years after Herft gave evidence to the royal commission, the diocese issued a statement saying Herft was under internal investigation for failing to report child sexual abuse to the police while he was bishop of Newcastle. The church said it was making its investigation into Herft public "in line with internal protocols" but it is unclear when the investigation began.

Abuse advocates and victims have previously been critical of the church's processes of investigating its own, questioning whether the process was fair and independent. The church has said the director of the Episcopal Standards Commission "is as independent as possible from the diocese but is paid by the diocese".

On Friday Archbishop of the Perth Kay Goldsworth issued a separate statement to the clergy acknowledging the internal investigation, but only after it was reported by the West Australian.

"I know you will continue to pray for all who have been affected by child sexual abuse," she said.