A CHURCH-GOING mum and her "humanist" ex-husband have fought in court over whether their son should go to a religious school.

The pair, from Melbourne, became bitterly deadlocked over the decision and asked a magistrate to decide.

The father told the Federal Magistrates' Court he opposed "organised religion" and didn't want it being thrust on his five-year-old son. He also argued he would not feel comfortable mixing with the school community because of his strong opinions.

The mother said a religious school was more likely to provide a strong and committed school community as well as a better education.

Magistrate Stewart Brown said it was "highly regrettable" he must decide an "intensely personal and sensitive issue".

"Although I may wish to avoid the issue of religion, in the determination of the case, I am unable to do so," he said.

Mr Brown ordered the boy to be enrolled at a religiously neutral school.

"The boy's tender years and ... issues of religious orientation at school, behove ... a cautious approach," he said.

Originally published as Son's religion an issue for court