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.
After today's hearing, the High Court is expected to hear Mr Francois' full legal bid later this year.
He will 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.
Meanwhile, the Secular Education Network said it has had a boost in membership since news of the hearing was published in the Herald on Sunday last weekend, alongside reports of a religious sex education pamphlet being used in a Christchurch school's health lesson.
About 60 new people joined the network in the 24 hours following publication of the reports, SEN spokesman David Hine said. New members will be among those demonstrating outside the High Court today.