The teacher at the centre of a police investigation was working at Otago Boys' High School until last week.
The Otago Daily Times contacted the school's rector, Clive Rennie, on Monday after confirmation police were investigating an alleged indecent assault.
Mr Rennie, in a joint statement with board chairman Geoff Bates, told the paper ''the teacher concerned is not currently at the school''.
Sources confirmed the teacher involved in the alleged indecent assault taught at the school until Friday, and left on Monday.
Yesterday, the ODT sought clarification as to the teacher's employment status.
Mr Rennie said he was not in a position to respond, while Mr Bates said the school was receiving legal advice.
The ODT understands the allegation is from a former pupil and dates back about 17 years.
Ministry of Education head of sector enablement and support Katrina Case confirmed the ministry was aware of the situation.
''The teacher has been stood down pending an investigation. The principal and the board chair are managing the situation, and we are available to provide any specialist support they may need.''
The Teacher's Council had been informed by the school, she said.
