The Church has written to each state-funded Catholic secondary school asking them to encourage pupils to sign a petition against gay marriages. In one school, pupils were shown a presentation on religious opposition to the planned changes which would allow couples to marry in civil ceremonies, saying it would reduce the significance of marriage.
The Catholic Eduction Service (CES) wrote to 385 secondary schools asking them to highlight a petition organised by the Coalition for Marriage, which is against gay marriage.
It has 466,000 signatures so far.
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, Sutton, told PinkNews.co.uk that pupils at her school aged between 11 and 18 had been encouraged to sign by their own headteacher, but in response, some children were wearing Gay Pride badges pinned to their uniforms:
"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 It was just a really outdated, misjudged and heavily biased presentation.
"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. After all, that's discrimination they were urging impressionable people to engage in, which is unacceptable."
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."