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But Damien Goodsir, who is also a pastor at Oamaru's House of Breakthrough, said he would remain as Fenwick School board chairman - and he backed the school's strong performance.
He announced his intention to resign from the two roles before a board meeting on March 14.
''I did it, not because I thought I did something wrong, but to help with the process. It was more like an act of good faith, more like 'I am willing to do that if it would help the school to be governed better','' Mr Goodsir said.
''The school numbers are growing - we're growing, growing, growing - so other than these two parents that are complaining, the majority of everything else is going really, really well and it's just that two parents are very unhappy with religion being in schools.''
The Otago Daily Times reported in December independent school governance consultant Cleave Hay would review the school to address ''continuing community concerns surrounding religious instruction, the roles of chaplains and some perceived conflicts of interest''.
At its meeting this week, in keeping with Mr Hay's report, the board decided to create a ''complaints handling committee'' for religious instruction complaints; committed to a three-yearly community consultation; stopped the chaplaincy roles at the school; and decided from 2018, religious instruction would move outside school class time hours.
It also decided to seek advice and support from the New Zealand School Trustees Association (NZSTA) on issues including complaints, managing conflicts of interest and community engagement.
NZSTA president Lorraine Kerr said yesterday the association ran ''comprehensive professional development for boards right around the country''.
And it was not uncommon for the association to assist on a range of issues to ''equip boards ... to be effective governance''.
Mr Hay visited Fenwick School on February 13 and 14 to conduct interviews with parents, staff and the board.
He declined to comment on his report, but did say ''it was just an objective view and what I felt would be the best for the community''.
He submitted his final report on February 28.
Mr Goodsir noted all motions were passed by the board unanimously and said he hoped the school could move on.
The Ministry of Education could not reply to the Otago Daily Times' questions before deadline yesterday, a spokesman said.
But in December the ministry's head of sector enablement and support Katrina Casey said ''a small group of parents'' had included the ministry in its communications with the school principal and board.
When a state primary school was open for instruction, the teaching must be entirely secular, but schools were permitted to close for up to 60 minutes per week, and no more than 20 hours in the school year, for the purposes of religious instruction or observance conducted by volunteers, she said.