The Christian Brothers' High School in Lewisham, near Sydney in New South Wales, says it was simply an academic exercise.
The practice has since been stopped.
The teacher in question, Jesse Pittard, teaches History and Geography lessons at the school and would read parts of the Koran before the school day began and before classes.
Daily Mail Australia reported that parents and pupils said he had read "more than half" of the Islamic holy book to them.
One mother told the paper her son was read excerpts before Geography lessons: "We don't send our kids to an Islamic school to listen to the Qur'an and it's not a religion lesson, it's a geography lesson, so how does that relate to geography?"
Mr Pittard did not comment.
The school's headmaster, Brother Paul Conn, says the teacher did read passages before some Year Seven classes.
He said he had received three emails and one phone call from worried parents, however he clarified that the readings that only happened "for a couple of days" and were an "academic exercise."
The head reassured parents: "We are one hundred percent committed to our Catholic faith, and that our strategic plan and Religious Education Program has the Catholic faith as its core."