Religious groups were under pressure on Sunday over allegations that the Catholic Education Service urged schools to back an anti same-sex marriage campaign.
The service, 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.
But the British Humanist Association (BHA) said that the proposal broke 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.
The BHA also confirmed it was considering pursuing legal action against the service over the matter.
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."
BHA campaigns officer Richy Thompson said: "On Thursday we wrote to Michael Gove and called for 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."
Mr Thompson added that the humanist association believed that "what has been done here is likely to have broken the Equality Act, as well as laws against political indoctrination."
But a CES spokesman defended the group's letter and insisted it had not acted illegally.
"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'," he said.
The news comes after the Pope called on Catholic leaders to form a broad alliance with Jewish and Muslim groups against plans to "redefine marriage."
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