He said the Bishop of Waiapu, Andrew Hedge, had "read these events through a prism very different to my own, and in dismissing me he has done what he thinks is right for the future of the church".
"I have a different opinion as to how a community of grace should work, but it is he, not I, who has that call. I will, therefore, take time out to consider my options for the future, and hope that my serious mistake 25 years ago may finally be laid to rest."
He said the liaisons had been with consenting adults, not as was originally alleged by church authorities in recent months, as predatory or with a minor.
Bishop Hedge said Dr Godfrey's behaviour was not related to the diocese of Waiapu.
Dr Godfrey, 56, was made dean in 2013. He had formerly been based in the Northern Territory of Australia and was archdeacon of Southern Rural Darwin, rector of the Parish of the Good Shepherd in Fred's Pass and chaplain at Kormilda College and Anglican secondary school in Darwin.
When appointed, he told Hawke's Bay Today he relished the challenge. He described himself as a "knockabout sort of a fellow" when it came to becoming engaged with the community and the varied roles he had taken up on his way to, and during, his clerical career.
He grew up on the Kapiti Coast and attended Wanganui Collegiate. He later studied for a Bachelor of Arts in English and religious studies at Massey University.
Among his credentials he had been a broadcasting cadet for Radio New Zealand, a specialist broadcaster in Adelaide and an auxiliary firefighter for the Queensland Fire and Rescue Service, which he was also chaplain to.
He would now not hold the office or perform any function of a priest "for a length of time yet to be determined".