According to 'The Age', the issue of banning the girls from running by the Al-Taqwa College in Truganina suburb was being probed by the state schools regulator Victorian Registration and Qualifications Authority (VRQA).
The report quoted a letter sent to the education ministers this week by a former teacher which claimed that female students were being discriminated against at the school.
"The principal holds beliefs that if females run excessively, they may 'lose their virginity'," the letter said adding "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".
Hallak had earlier also claimed that Israel and the US had conspired to create the Islamic State terrorist group, The Age reported.
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The issue has been referred to both federal and state education ministers.
Victorian Education Minister James Merlino said he was not aware of receiving the letter, but has referred the claim to VRQA to investigate.
"There are minimum standards that school's must meet, including minimum standards of governance. I've asked the VRQA to investigate to determine whether these reports are true and if they are, to report back to me and what further action could be taken," he said.