Education secretary Michael Gove is to investigate allegations pupils as young as 11 were urged to sign an anti-gay marriage petition at their school.
Last week, the Catholic Education Service (CES), which promotes Catholic education, confirmed it wrote to 359 state schools in England and Wales to remind them of the traditional definition of marriage.
The British Humanist Association has since claimed the move may break equalities legislation - an accusation the CES has vehemently denied.
A spokesman for the Department for Education said on Sunday that it was looking into the complaints.
"Schools have a responsibility under law to ensure children are insulated from political activity and campaigning in the classroom," the spokesman said. "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."