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.

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.

"The comments of the al-Taqwa College principal are wrong and damaging," he said.

Ajit Somers taught at the school in 2001 and said Mr Hallak had "shockingly" anti-Semitic views.

He said the principal came into his class and set an assignment in which students had to research a country of their choice. When the principal discovered one student had chosen Israel, he became furious, Mr Somers said.

"He said there is no such thing as Israel and how dare you say Israel. He said Jews are horrible people."

After Mr Hallak left the room, Mr Somers said he told students Israel existed and was a member of the United Nations.

A number of former al-Taqwa teachers have raised concerns about the principal's views following revelations by Fairfax Media last week that he told students not to join Islamic State because it was a plot by Western countries.

He then went on to say that he believed IS was a scheme by Israel and the US.

Another former teacher at the Truganina school in Melbourne's outer west, who did not want to be named, said teachers who were not Muslim were treated as "second-class citizens".

The teacher said she was told off by the principal after she drew a star on a whiteboard to reward good work.

"He said 'that is a Jew symbol. If you do it again I will kick you out'."

Mr Hallak has been called to a meeting with state government officials to explain why he told students that IS was a plot by the West.

State government officials will meet the college after the school holidays to "develop a program of cross-cultural understanding".

Mr Merlino said earlier this week that the principal's comments were "a real concern".

"The comments made have no place in our schools and we look forward to working with the school community to address the issue."

Mr Hallak did not respond to questions.

The Truganina school received $11.2 million in federal government funding in 2013, and $4.7 million from the state government, according to the My School website.

In 2005 The Sunday Age reported that a visiting imam told al-Taqwa students that Jews were putting poison in bananas and they should not eat them.

henrietta.cook@fairfaxmedia.com.au