Federal Education Minister Christopher Pyne has asked the principal of al-Taqwa College to explain why he told students that Islamic State was a Western plot.

The move comes as a former teacher at the school said principal Omar Hallak also told students that Israel did not exist and Jews were horrible people.

Al-Taqwa headmaster Omar Hallak

Mr Pyne condemned the principal's controversial statements on Wednesday and said he would write to al-Taqwa, which is the largest Islamic School in Victoria, seeking an explanation.

Mr Pyne will also write to Victorian Education Minister James Merlino to ask what action the Education Department is taking.