“When I started this journey to right the wrongs of child abuse in the diocese I didn’t expect to be in this position, nor did I expect to uncover systemic practices that have enabled the horrendous crimes against children,” Bishop Thompson said in a statement released to the media on Thursday morning.

“The decision to resign was not an easy one, it weighed heavily on my heart. However, I must place the wellbeing of my family and my health above my job.”

He is the second senior member of the diocese to resign for their strong opposition to child sexual abuse in the diocese, after former diocese business manager John Cleary resigned on February 27. Mr Cleary was recognised by the diocese for being “dedicated and diligent in uncovering child sexual abuse in the diocese and providing crucial support to survivors”.

Both men told a royal commission public hearing in Newcastle in August and September of uncovering harrowing child sexual abuse involving clergy and church representatives over decades, shocking cover-ups and appalling opposition when they tried to uncover the truth and change diocese culture.

The hearing included exposure of a letter by leading diocese members, including former Newcastle Lord Mayor John McNaughton, solicitor and synod member Greg Hansen, synod member Laurie Tabart and church wardens Simon Adam and Andrew Traill, to Royal Commissioner Justice Peter McClellan, questioning why Bishop Thompson had taken many years to reveal he had been sexually abused by clergy as a teenager.

The public hearing included a torrid exchange between Justice McClellan and solicitor Robert Caddies, during which Justice McClellan accused Mr Caddies of leading “coordinated opposition” to Bishop Thompson.

The group also complained to Sydney Anglican Archbishop Glenn Davies, who is expected to give evidence next week during the Royal Commission’s final hearing into the Anglican Church in Australia, including its responses to allegations of child sexual abuse.

Bishop Thompson will give evidence on Friday in a panel that includes Sydney University Professor of Law Patrick Parkinson, and Brisbane Archbishop Phillip Aspinall.

Newcastle Anglican diocese professional standards director Michael Elliott will give evidence next week.

Bishop Thompson told the Newcastle Herald in September that he became the “bishop not welcome in his own cathedral” because of opposition to his attempts to change the diocese’s culture on child sexual abuse.

Justice McClellan’s fiery questioning of Mr Caddies was “a validation”.

“It was a gift to be publicly validated,” the bishop said.

“Although it was only 20 minutes of evidence it was a message to those who had sent the letter. They weren’t going to walk away without knowing how it had been received.”

Bishop Thompson was announced the new Anglican Bishop of Newcastle in October, 2013, after difficult years under the leadership of Bishop Brian Farran, whose tenure was dogged by child sexual abuse scandals, including the defrocking of former Dean of Newcastle Graeme Lawrence.

The defrocking process led to a Supreme Court appeal against the diocese, which Mr Lawrence lost.

In an interview with the Herald in August, 2014 Bishop Thompson first spoke about being an abuse victim, and named the late former Bishop Ian Shevill as his abuser.

The following June he made an historic apology to child sexual abuse survivors in the diocese, and revealed that up to 30 perpetrators over four decades molested children - including the children of priests.

He marked his 500th day as head of the church in the Hunter by telling clergy "We can't have mates looking after mates any more".

Since the end of the Royal Commission’s Case Study 42 on the Anglican Diocese of Newcastle I’ve been reflecting on the important work of the Royal Commission and the change underway in the Diocese of Newcastle and its impact on my health,” Bishop Thompson said in his statement on Thursday.

“It has been widely documented in both the media and the Royal Commission how the culture and conduct from some sections of the church has had an impact on survivors, families, and communities across the Diocese of Newcastle.

“I have witnessed this culture first hand, both as victim of abuse and in my work as Bishop to address the Diocese’s abuse legacy.

“The decision to resign was not an easy one, it weighed heavily on my heart.”

Bishop Thompson has worked in the church for 38 years and said he had “enjoyed the many exciting roles he had served in during that time”.

He established the parish recovery teams to work with church communities to change church culture.

“I have confidence in the present church leadership of this Diocese who have stood with me in wanting to face the past and shape a healthy future. I could not have done my work without their professional and dedicated support for change,” Bishop Thompson said.

He will formally end his tenure on May 31. Bishop Peter Stuart said in a statement that the diocese will hold a special session of Synod on May 20 to consider the election process, after a Synod of the diocese in 2014 indicated it wished to change some of the process by which a bishop is elected.

Bishop Stuart expressed the diocese’s “considerable sadness at the news that Greg Thompson won’t be returning to ministry as the Anglican Bishop of Newcastle”.

”In his short time as our Bishop he has been the catalyst for deep cultural change around the protection of children and the support of victims of abuse. He called us to face our past and in doing so shape a healthy future. This will be his enduring legacy,” Bishop Stuart said.

“As part of shaping a healthy future, we worked together in November to initiate independent external reviews of diocesan governance and the professional standards and redress processes. These reviews are well underway and will continue the crucial work of transforming the Diocese.

“Bishop Greg has led the Diocese to greater health.”

He said the diocese had “rejoiced that a son of the diocese had been elected as bishop”.

“The clergy and people have delighted in his ministry in parishes, at the diocesan convention and synod. We have felt deep anguish for him and his family as we learnt of the abuse he experienced and the rejection by some in the Diocese,” Bishop Stuart said.

“Throughout his ministry he has been committed to hearing the voices at the grassroots and empowering the vulnerable and people in need. Drawing on the great treasures in the teachings of Jesus, he has been unafraid of speaking strongly to the powerful to ensure transparency and promote justice.

“We are deeply thankful for Bishop Greg Thompson’s ministry as Anglican Bishop of Newcastle. Our thoughts and prayers are with him and his family in this time of transition.”