A group which is against religion being taught in schools has stepped up the fight against the Federal Government's school chaplaincy program.

Yesterday the High Court found the program's funding arrangements are invalid, but rejected arguments against the program on religious grounds.

Proselytising is banned under the school chaplain's program, but a lobby group is pointing to evidence which suggests some chaplains believe they are on a covert mission to spread God's word.

The Government has vowed to find a way to keep the program alive, but Scott Hedges from Fairness in Religions in School says there is evidence some school chaplains are working to convert children to their church.

Mr Hedges points to a speech by an Access Ministries chaplain which he says was recorded by Access Ministries last year.

In the speech, the chaplain mentions the program as a covert way of spreading God's word.

"So remember it is God's hand within and across our schools through the commitment of Access Ministries. Access Ministries provides Christian religious education teachers and chaplains to over 2,000 young Victorians in our schools," she said.

"Now that is not always overt, CRE (Christian religious education) workers are definitely there to present the gospel, to present bible stories. Chaplains - it is not always as overt as that, it is much more covert."

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The Federal Government has already investigated Access Ministries, after the group's chief executive, Evonne Paddison, told a conference - ''we need to go and make disciples".

That investigation found no evidence that chaplains tried to convert students in breach of government guidelines, but Mr Hedges is not convinced.

"I mean, I think it is very unreasonable for the Government to hire people explicitly because they're Christians and then expect that they are not going to advance their beliefs on young children, especially children who are having trouble," he said.

He says the definition of proselytising is too vague and allows organisations to work around it.

"The problem with proselytising is that it is a word - nobody really knows what it means," he said.

"When do you know that somebody is just telling you what they think versus proselytising? It is just a terrible concept."

The ABC's attempts to contact Access Ministries have been unsuccessful.