An Anglican bishop and advocate for child abuse survivors is resigning after being subjected to harassment, including being warned about his personal safety.

Greg Thompson will step down as Newcastle bishop to focus on his health after being ostracised by some of his own parishioners since revealing he was abused as a young man by senior church clerics.

Thompson said he had witnessed firsthand the culture and conduct from some sections of the church, both as an abuse victim and in his work to address the Newcastle diocese’s abuse legacy.

“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,” he said on Thursday. “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.”

The child abuse royal commission has heard of a deep division in the Newcastle diocese, with some people believing a number of priests were unfairly disciplined over sex abuse allegations.

Thompson has told the inquiry people of power and influence provided a protection racket during decades of abuse by clergy and lay people in the diocese.

He said the criticism, threats and harassment had taken a toll and he had security installed in his home because he did not feel safe.

“In those intimate moments in church – it is my cathedral – having people turn their backs on me sends a strong message that I’m not safe in that place and that there are consequences if I do not follow what they want me to do. Public harassment. Public shame.”

A group of influential parishioners wrote to the royal commission questioning the timing of Thompson’s abuse claims, saying he could have put other young people at risk by waiting until 2015 to come forward.

Thompson, who has been the Newcastle bishop for three years, has been on leave since giving evidence to the royal commission in November.

Newcastle assistant bishop Peter Stuart said Thompson had been unafraid to speak strongly to the powerful to ensure transparency and promote justice.

“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,” Stuart said. “He called us to face our past and in doing so shape a healthy future. This will be his enduring legacy.”

Thompson’s resignation takes effect on 31 May. He will be among church leaders giving evidence to the royal commission’s final Anglican hearing that begins in Sydney on Friday.