The country's only co-educational Islamic school has been put under direct Government control amid concerns that its cultural environment is clashing with its education obligations.
Al-Madinah School in Mangere, Manukau City, has been under fire for several years for prioritising religion at the expense of the curriculum and segregating staff and students according to gender.
Successive Education Review Office reports have drawn attention to problems of "governance and segregation", and a limited statutory manager was installed in 2002.
But the Ministry of Education has now drafted in Dennis Finn - the man who took over at troubled Cambridge High School last year - to haul the 360-student school into line.
Melissa O'Carroll, the acting northern region manager for schools, said Mr Finn's appointment as commissioner was "to support the school and enable it to strengthen educational outcomes for all its students".
The school has made concessions to the review office. It reversed a 2003 decision to cease education for girls beyond Year 8 and last year extended the length of the school day to accommodate prayer and lessons.
But a new ERO report has sparked the overhaul, with Education Minister Trevor Mallard dissolving the board of trustees after seeing the report.
Some parents are angry the report has not been made public. Syed Iqbl Nabi, who has a 6-year-old son at Al-Madinah, said either the Government or the school should have told everyone what was happening.
He said it was a good school which offered a good education combined with appropriate discipline.
However, other Muslim parents had concerns about the school.
Dr Saad Al-Harran took his son out of Al-Madinah after just two weeks. He said the school had a "narrow interpretation" of the Islamic faith. Communication and management were very poor.
Another father said the problems were caused by divided cultures within the Islamic faith. There was distinct and growing animosity between "normal" Muslims and Wahabis (a puritanical sect) within the school, he said.
Mr Finn said the special character of the school had to be considered, but it was integrated into the New Zealand system "and needs to meet the education requirements".
Principal Asin Ali remains at the Year one to 13 school, where 45 per cent of students are Fijian Indians, 16 per cent Somali and 14 per cent Indian.