Rotary Park School principal Carmel Casey has gone on paid leave until further notice.
Mrs Casey requested leave last week and was granted it, Cleave Hay, the commissioner steering the school through troubled waters, said. She left at the end of the following day, just one day before the end of the first school term.
Her leave was "discretionary leave as allowed for in her employment agreement", Mr Hay said.
Parents were informed in a newsletter last Wednesday.
Mrs Casey has been at the centre of allegations of incompetent teaching practices and staff bullying. Matters came to a head at the start of this year when parents and staff learnt she was returning to the school after six months' leave.