The Roman Catholic church has written to every state-funded Catholic secondary school in England and Wales asking them to encourage pupils to sign a petition against gay marriage.
Students at one south London school were shown a presentation on religious opposition to government plans to let gay couples marry in civil ceremonies.
Church leaders believe the proposal would reduce the significance of marriage.
The Catholic Education Service, which acts for Catholic bishops in England and Wales, contacted 385 secondary schools to highlight a letter read in parish churches last month, in which two archbishops told worshippers that Catholics have a "duty to do all we can to ensure that the true meaning of marriage is not lost for future generations".
The CES also asked schools to draw pupils' attention to the petition being organised by the Coalition for Marriage, a Christian campaign which has attracted more than 466,000 signatures to date.
Terry Sanderson, president of the National Secular Society, said: "This is a clear breach of the authority and privilege that the Catholic Education Service has been given in schools. Surely it is no part of its remit to promote a specific political campaign from this purely sectarian viewpoint. It is disgraceful that children are being encouraged into bigotry when they are attending a state school paid for by taxpayers."
A pupil at St Philomena's Catholic high school for girls in Carshalton, in the south London borough of Sutton, told the website PinkNews.co.uk that children aged 11 to 18 had been encouraged to sign the anti-equality pledge by their headteacher.
She said: "In our assembly for the whole sixth form you could feel people bristling as she explained parts of the letter and encouraged us to sign the petition. It was just a really outdated, misjudged and heavily biased presentation."
She said some pupils had responded by buying Gay Pride badges to pin to their uniforms. "There are several people in my year who aren't heterosexual – myself included – and I for one was appalled and actually disgusted by what they were encouraging," she said.
"After all, that's discrimination they were urging impressionable people to engage in, which is unacceptable."
The British Humanist Association said the CES's actions were likely to be in breach of sections 406 and 407 of the 1996 Education Act, which ban the political indoctrination of schoolchildren and require political views to be presented in a balanced way.
The Act was used in a failed attempt to prevent schools showing Al Gore's climate change documentary An Inconvenient Truth.
The BHA's faith schools campaigner, Richy Thompson, said: "This action by the Catholic Education Service is absolutely outrageous." Thompson said the church has undermined "one of their core arguments against gay marriage, which is supposedly to protect children from exposure to such matters".
A CES spokeswoman said: "We said that schools might like to consider using this [letter] in assemblies or in class teaching. We said people might want to consider asking pupils and parents if they might want to sign the petition. It's really important that no school discriminates against any member of the school community. Schools with a religious character are allowed to teach sex and relationships – and conduct assemblies – in accordance with the religious views of the school. The Catholic view of marriage is not a political view; it's a religious view."