The Secular Education Network, which is supporting Mr Warren, said a second parent at St Heliers School had now laid a complaint about the religious instruction programme.
Spokesman David Hines said the classes, also known as Bible in Schools, took place in about 800 state primary schools nationwide.
"This is believed to be the first time a parent has taken a complaint about it to the Human Rights Commission,'' he said.
The commission would not comment because of the confidential nature of mediation, a spokeswoman said.
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Religious instruction in state schools
* Teaching must be secular during the hours a school is open for instruction
* Schools can close for up to an hour a week to a maximum of 20 hours a year for religious instruction or observance
* Children can opt out of classes if parents don't want them to take part
(Source: Human Rights Commission)