She acknowledged the ministry may not have been notified about other concerns.
"If parents have a complaint they should talk to the principal in the first instance and then, if not satisfied, raise the matter with the board of trustees.
"We would encourage any parent to try to resolve any issues with the school and board of trustees before taking further action.''
Schools involved in the complaints held religious classes during teaching hours. Pupils' parents had to choose to opt out their child if they did not want them to attend.
The Secular Education Network, which is opposed to Christian teaching during schooltime, said that meant children who did not go to the lessons would feel ostracised from their friends.
Those children were also often offered "meaningless activities'' during the classes, the group's spokesman David Hines said.
Earlier this year two Auckland parents complained to the Human Rights Commission about St Heliers School offering the classes. A third parent lodged a formal complaint with the school.
Mr Hines said since then parents with children at Auckland's Glendowie School, Palmerston North's Milson School and another Palmerston North school, which has not been named, had complained to school leaders about the classes.
The Churches Education Commission supplied teachers to the schools at the centre of the complaints.
Chief executive Simon Greening said boards of trustees needed to follow a "fair and democratic process'' when dealing with the future of the classes.
"We do not want to be in schools where our Christian values classes are not welcomed,'' he said.
"But on the other hand, we believe it is undemocratic and a loss to Kiwi kids if our classes are closed without a fair process.''
Changes made by the schools:
* St Heliers School - moved CRI classes to outside school hours;
* Milson School - moved CRI classes to outside school hours;
* Glendowie School - offering more research options, such as use of library computers, for students not attending the classes
* Unnamed Palmerston North school - consultation between board and complainant later this month.