Education officials are looking into whether the Catholic Education Service (CES) broke any laws by asking schools to encourage children to back a campaign against same-sex marriage.
The CES, which acts for Catholic bishops in England and Wales, wrote to every state-funded Catholic secondary school in England and Wales asking them to back the petition by the Coalition for Marriage.
The British Humanist Association (BHA) suggested the move breaks sections of the Education Act 1996 regarding political indoctrination and requirement for balance, and a section of the Equality Act 2011 regarding public sector equality duty.
It said it has expressed interest in taking a legal case on the matter, and is looking for a pupil to help.
A Department for Education spokesman said: "Schools have a responsibility under law to ensure children are insulated from political activity and campaigning in the classroom. While faith schools, rightly, have the freedom to teach about sexual relations and marriage in the context of their own religion, that should not extend to political campaigning. Officials are looking into this as ministers are anxious to establish the full facts of this case and will be meeting representatives of the CES shortly."
The BHA welcomed the news. Faith schools campaigner Richy Thompson said: "On Thursday we wrote to Michael Gove and called for just such an investigation. We are glad to see that this is now occurring. Any gay, lesbian, bisexual or transgender pupil at a school whose head declares that gay marriage and civil partnerships are unnatural is obviously going to feel discriminated against and trapped. Action to remedy this situation cannot come soon enough."
But he added: "The BHA believes that what has been done here is likely to have broken the Equality Act, as well as laws against political indoctrination. The Government's statement suggests that only the latter area is being considered, which unfortunately fits with past behaviour. We hope that the Government will fully consider both areas of legislation."
In a statement, the CES said: "The Archbishops' letter was circulated to all Catholic parishes and secondary schools. The letter is a positive affirmation of marriage, as is the Coalition for Marriage's online petition. As the letter says, Catholics believe that 'marriage is a high and noble vocation'.
"We reject the suggestion that Catholic schools have acted illegally. The Equality Act 2010 applies to all schools and we are fully supportive of the Act. It is central to Catholic teaching that all individuals should be treated with respect and dignity.
"Catholic state schools have always been permitted by law to teach matters relating to sex and relationships education, including the importance of marriage, in accordance with the teaching of the Catholic Church. The Catholic Church's view on the importance of marriage is a religious view, not a political one. The online petition itself makes it clear that people under the age of 16 cannot sign it. We will issue new guidance for our schools to ensure that they are aware of this."