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She is the sixth Dunedin secondary school principal to have resigned or retired in the past 12 months.
The 56-year-old's resignation was announced to surprised staff and pupils at the school during a formal assembly yesterday morning, where she announced she would take up a new position as the director of education for Otago and Southland.
The ministry had not given permission for her to give details yet, but she was excited about the challenges the position would provide.
It would be an opportunity to use her skills to make a difference at ''the wider systems level'', she said.
''I have been at Queen's for nine years and I expected to stay for another nine years until retirement age.
''Schools are very hard places to leave, but the success of a school should never depend upon one person.
''A school is about a team and a community effort.''
Mrs Anderson said a principal's role was to build capacity and leadership in the pupils, the teachers, the board and the community, and the school was on a roll at the moment.
''I know it will continue to thrive.''
Mrs Anderson is the latest in a string of principal/rector resignations and retirements in the past 12 months.
John McGlashan College principal Mike Corkery retired at the end of last year, Taieri College acting principal Paul Bolton resigned in mid-2013, and Columba College principal Elizabeth Wilson, St Hilda's Collegiate School principal Melissa Bell and Otago Boys' High School rector Clive Rennie have announced they will be leaving their positions later this year.
Otago Girls' High School, King's High School, Kavanagh College and Bayfield High School have also had changes of principals in recent years.
Logan Park High School principal Jane Johnson is the only remaining long-serving principal, and despite being at the school for 16 years, she said she had no plans to resign or retire.
Explaining why many positions for principals were becoming vacant, Mrs Johnson said many Dunedin secondary schools appointed new principals about 16 years ago, and it was logical they would all be ready to move on about the same time.
Mrs Anderson planned to start her new job in early August, by which time it was hoped the Queen's High School board of trustees would have appointed her replacement.