The prayer, which said that children had the right "to fully benefit from the love of a father and a mother", drew protests of homophobia from gay rights groups and allegations that it was a political initiative that overstepped the bounds of France's official secularism.
"This prayer does not exclude anyone," Mgr Bernard Podvin, spokesman for the bishops' conference, told French television.
"It's no scoop to report that the Church opposes homosexual marriage. There should be a debate. But there isn't one."