The lawyer for a man trying to remove religious instruction from schools has used the analogy of David and Goliath, after the country's largest Bible-studies provider joined the battle against his client.

The Churches Education Commission (CEC) launched its legal challenge in the High Court at Auckland this morning to be allowed to give evidence in a spat between Jeff McClintock and the Attorney General.

Mr McClintock believes his daughter was segregated and humiliated after opting out of religious studies at Red Beach Primary School.

His lawyer Richard Francois is seeking to repeal Section 78 of the Education Act, a move which could lead to religious studies being removed from state schools.

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In court today, he said the proposed inclusion of CEC as an interested non-party was "intervening and ganging up on my client".

"This is a little man up against a giant - the government with all its panoply of power."

He labelled Mr McClintock as "David" and CEC's lawyer Ian Bassett said he appreciated the "ironic biblical reference".

But Mr Bassett rejected the notion that the non-denominational charitable trust was bullying the plaintiff.

He said CEC provided programmes to 667 state schools, though Red Beach was not one of them.

"This proceeding is going to be the vehicle for a broad range of criticisms of Christian religious education programmes nationwide," Mr Bassett said.

If Mr McClintock's legal action was successful, he said it would have a huge impact on CEC's future.

But Mr Francois was sceptical.

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"To say, rather dramatically, it'll have a chilling effect, it's just not sound enough," he said.

"You'd have to have a lot of evidence about that and I don't know where you'd get that from."

The main issue, according to the lawyer, was the difference between religious education and religious instruction.

"Religious education is about teaching children about religion and how it influences art, literature, civilisations, the history of religions, how it affects other groups of people," Mr Francois said.

"Religious instruction, however, is Bible-based. It's doctrinal, it's about instruction and is taken by a person of Christian faith. It's not taken by a teacher."

The High Court is expected to hear the full legal bid later this year and Justice Susan Thomas reserved her decision as to whether CEC would be joined.

Mr Francois 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.

He told the court today that that was "quality teaching time lost", which Red Beach Primary School was particularly in need of, according to ministry statistics.