The schools regulator, the Victorian Registration and Qualifications Authority, is investigating the allegations, which have been referred to the state and federal education ministers.

It follows revelations in The Age last month that the principal of the Islamic school, Omar Hallak, told students that Islamic State was a plot by Western countries.

In a letter sent to the education ministers this week, a former teacher said female students were being discriminated against at the Truganina school.

"The principal holds beliefs that if females run excessively, they may 'lose their virginity'," the letter said.

"The principal believes that there is scientific evidence to indicate that if girls injure themselves, such as break their leg while playing soccer, it could render them infertile."

The former Al-Taqwa teacher said Mr Hallak prevented the female primary school cross country team from participating in a 2013 and 2014 district event.

They said Mr Hallak was unaware that female students had been training for the event and intervened when he realised they were set to compete.

The teacher said they had worked at another Islamic school where female students were encouraged to take part place in any sporting event.

"I look back on my time at Al-Taqwa with frustration and anger, which is how I felt most of the time while I was working there. I did my best to stay committed to the students however in the end, I was unable to provide the same opportunities to students that I was given when I was at primary school, more than 20 years ago."

Concerned female students expressed their concerns in a handwritten letter to the principal, saying it was unfair that the cross country event had been cancelled.

"It was really shocking to find out it has been cancelled because of the excuse girls can't run," the students said.

"Just because we are girls doesn't mean we can't participate in running events. It also doesn't say girls can't run in the hadith (the sayings of Muhammad)."

The students said parents were annoyed by the decision and "think that girls and boys should both be allowed to participate equally."

Another former Al-Taqwa College teacher backed the claims. "I was told the girls weren't allowed to participate. The reason was they might over-exert themselves and lose their virginity or be rendered infertile."

Hannah, a parent of two girls at the school, defended Al-Taqwa College and said her children participated in sport.

"They do basketball, they run around the school, they do everything, but when they sack one teacher, they can say whatever they want," she told 3AW.

She said the claims were "rubbish" and made her feel sick as both a mother and a Muslim.

When asked whether girls were banned from running in the cross country, she said "I'm not so sure".

Mr Hallak told The Age last month that he believed IS was a scheme by Israel and the US to control oil in the Middle East.

henrietta.cook@fairfaxmedia.com.au