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Wayne Bosley has been at the school for twenty years but has been under the spotlight in the past few months following a very poor Education Review Office report last year.
More recently, there were calls from a group of parents of students for the Ministry of Education to investigate what they described as a lack of governance, and a vote of no confidence in Mr Bosley.
In his resignation letter to parents, caregivers and students Mr Bosley said he had informed the Board of Trustees that he will continue to work through to the end of the school term and would then step down for the transition to a new leader.
"I am humbled to have played a role in the development of so many students as they matured into wonderful people who are making such a positive contribution to society. I am hugely grateful for the support from staff, boards of trustees and members of the Upper Clutha community during my tenure at MAC," Mr Bosley wrote.