The circumstances of his departure are unclear.
His departure, announced in a joint statement with commissioner Nicola Hornsey yesterday, comes after a 12.5% drop in enrolments was predicted at the school next year, which will result in cuts to teaching jobs and $100,000 less funding.
Ms Hornsey was appointed commissioner of the embattled school in October last year, after its board of trustees stepped aside and two independent reports and an Education Review Office review criticised the way the school was being governed and managed.
Last month, Ms Hornsey cited ''a culmination of events'', including an ageing population in the area and the school's ''tarnished'' public image as contributing factors to the predicted decline in enrolments.
Ms Hornsey said Mr Jackson had demonstrated professionalism and maintained silent dignity in the face of very public discussion about his management of the school ''in circumstances that meant he did not have the opportunity to respond''.
Ms Hornsey said Mr Jackson had made several changes at the school that were requested by the board of trustees, including the introduction of the Cambridge curriculum to increase the number of academic scholarships and excellence endorsements awarded to pupils.
He had also been involved in a significant upgrading of the school's IT infrastructure, which was under way, and had pushed the development of the Fraser farm.
''[It is] now a fully irrigated productive farm that provides hands-on learning opportunities for students,'' she said.
Neither Mr Jackson nor Ms Hornsey returned calls yesterday and in a statement said they would not be available for further comment this week.
No-one was answering the door at the school's rectory yesterday.
