"It seems only fair that we are allowed to have a say in this important case, which could have many implications," said commission spokeswoman Debra Hunt.
The legal challenge was launched by the McClintocks after their daughter Violet was made to sit alone in a corner of her Red Beach School's classroom, kneeling on the floor reading a book next to the rubbish bin, after her parents opted for her to sit out religious studies.
Red Beach is not one of the 667 schools CEC provides studies for, a group of schools which have an estimated 65,000 pupils on their rolls. Francois, an Auckland lawyer who is taking the case pro bono, questioned what the body would "add" to the legal challenge.
After Thursday's hearing, the High Court is expected to hear Francois' full legal bid later this year.
He said he would challenge the Education Act's legality, arguing Section 78 was in breach of the Bill of Rights and discriminated against pupils who did not hold Christian beliefs. This section allows schools to close up to an hour a week for religious instruction.
Children were drawn into the religious classes as they didn't want to be seen as different, Francois said.
"So even if their parents opt them out they may go against their parents' instructions."
Francois believed the lost teaching time undermined children's performance in core subjects.
"We say the board of trustees have made an erroneous decision to allow these Bible in schools groups to participate in religious instruction during school hours."
Those children who opted out of class were sent to the library or treated in a "punitive" way, including being sent to pick up rubbish or do dishes, he said.
Violet's father, Jeff McClintock said Bible in schools was an extra-curricular activity and taking up class time was not justified by law.
"The kids are simply missing out [on] class time each week which they're entitled to."
After four years of conflict, 9-year-old Violet has left Red Beach School. She was now studying at a neighbouring school with her younger brother.
That school did not have Bible in schools study.
The Education Ministry said it would be inappropriate to comment as it was a party to the case before the courts.
The rules
• Parents can choose to withdraw their children from religious instruction.
• Schools are able to offer one hour a week of religious studies.
• Each school decides on whether Bible programmes are offered.
• Schools can schedule them at whatever time suits.
