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The ministry appointed Dunedin man Cleave Hay as limited statutory manager for the school several weeks ago, after discord arose at governance level towards the end of last year.
A committee has governed the board since former chairman Richard Cubie resigned in December, citing his concern over the way the school had dealt with complaints from parents.
Mr Hay announced to staff and parents yesterday Mr Thomas had been unanimously elected as chairman at a special board meeting on Tuesday.
Mr Thomas is a parent-elected trustee who has been on the board since the general elections last year and has experience through his career in chairing groups.
''He is a well known and respected member of the community through both his career and community activities,'' Mr Hay said.
Principal Wendy Bamford said she looked forward to working with Mr Thomas ''in moving our school forward''.
Mr Thomas said he too was looking forward to working with the board, Dr Bamford and staff, in conjunction with Mr Cleave, in his new role.