Islamic schools across the country will be investigated by the federal Department of Education after a string of sackings among senior staff members and principals, allegations of financial mismanagement and concerns over the delivery of the curriculum.
Education Minister Christopher Pyne said the department has commissioned an audit of all six schools to "get to the bottom of these matters".
"I'm concerned with allegations reported in the media in relation to curriculum, gender segregation, senior staff movements and financial transactions," he said. "We want to be confident that schools operate in the best interests of their students."
The six schools receive up to $45 million a year from state and federal governments, some of the highest levels of taxpayer funding in the country.
They are all affiliated with the largest provider of Islamic education in Australia – the Australian Federation of Islamic Councils (AFIC) – which has come under years of scrutiny by state education departments for its governance and administration.
One of the schools under investigation is the largest Islamic school in Australia, Malek Fahd in Sydney's south-west, which educates up to 2500 students each year.
The Greenacre school came under the microscope in 2013 after it was forced repay $9 million in NSW government funding because it was found to be inappropriately transferring money to AFIC.
The latest investigation caps off a controversial week for the school after it began pursuing a student it had expelled in the NSW small claims court for $490 in unpaid school fees.
The school asked the student to leave in 2011 after it told his parents his academic performance was "deemed insufficient" following a report that suggested he was unlikely to get an ATAR above 80.
In his statement of claim the boy's father has described the schools actions as "astonishing and unjustifiable".
Five other schools associated with AFIC will come under the audit including the Islamic College of Brisbane, the Islamic College of Melbourne, the Islamic College of South Australia, the Islamic School of Canberra and Langford Islamic College in Western Australia.
A letter sent to the schools said auditors would visit the next week. The letter said the schools must provide "full and free access" to records relating to financial administration.
Two schools in NSW that have come under fire from the NSW Department of Education have escaped the federal investigation, despite the ongoing concerns of parents and regulators.
Al Noori Muslim School in Greenacre has until December to show it has addressed the Board of Studies' concerns over financial transactions and governance by the school after a series of property deals in 2012 with the school's chairman were brought to light.
The school's funding was frozen for a year, but has since been restored. The school has denied any wrongdoing.
Rissalah College in Lakemba has also come under scrutiny from the NSW department after its former chairman brought allegations of financial mismanagement to light in a case that was settled in March.
Rissalah's funding was frozen in 2013 but was restored a year later after veteran principal Bill McKeith was parachuted in by the Association of Independent Schools to do an "emergency repositioning of the school".
Dr McKeith has has since openly criticised the board's structure and its governance policy.
"The board did not have the variety of skills and backgrounds required to be an effective board," he said.
Watch: Dr McKeith at Rissalah College
The former chairman, Bassam Kamaledine, has urged federal and state authorities to re-investigate the college after teachers said there were constant warnings of a "lack of funds" which forced them to pay for their class photocopying at the local Officeworks.
One senior teacher said that funds were so tight at the school that staff were asked to cut stamps out of used envelopes that had been thrown in the bin and reuse them.
"There was a lack of everything, from intra-school sports to excursions," said a parent of one child who has been at the school since kindergarten.
The father, who asked not to be named, said there was a "toxic culture of silence" within the community in which people were fearful of speaking out.
The school has also gone through three different principals in the past year.
"There has been no explanation from the school in relation to any of its actions and that is unacceptable," said a father of a child in year 5.
Rissalah College has declined to comment.
