The Principals Federation says state primary schools should consult thoroughly with parents before offering religious classes, to avoid any conflict.
Two parents at St Heliers School in Auckland have laid complaints with the Human Rights Commission about Christian education classes the school offers five and six year-old pupils.
One of them Melissa Muirhead says the children are too young to question what they're told during the classes and accept it as fact.
Federation president Phil Harding says schools can offer religious classes during the school day but technically must be closed when they do so. He says he's seen the issue cause bitter divisions within schools.