The rare clerical foray into political debate, on the Assumption Day holiday observed in traditionally Catholic countries in Europe, referred only indirectly to the new marriage law the government plans to pass next year.
But the carefully worded text, first published earlier this month, dominated the news headlines in France, where the media have presented it as a strong attack on the reform.
Church leaders insisted their aim was to launch an open debate about plans to legalise same-sex marriage and euthanasia, two in a list of 60 pledges made by Francois Hollande in his successful election campaign for the presidency last spring.
"The Church wants a debate about social reforms that are coming soon and that really worry us," Monsignor Bernard Podvin, spokesman for the bishops' conference, told LCI television.
"This prayer does not exclude anyone," he said.
Gay rights groups disagreed.
"This message is fertile ground for discrimination and homophobia," Michael Bouvard of the SOS Homophobie group told LCI. Secularists have also asked if the Church should publicly take sides in a political debate.
The prayer echoed the defence of traditional marriage by Pope Benedict and Catholic leaders worldwide as gay nuptials gain acceptance, especially in Europe and North America.
Underlining this link, a senior Vatican official led the traditional vigil Mass on Tuesday evening in Notre Dame Cathedral in Paris, before a procession of tourist boats on the Seine River, and read out the disputed prayer.
Archbishop Rino Fisichella is head of the Vatican's "new evangelisation" campaign meant to raise the Church's profile and win back believers who have left it in droves in recent decades.
The government has pledged to legalise same-sex marriage, which polls say 65 percent of French people support, in the first half of 2013.
Same-sex and heterosexual civil unions, with fewer rights than marriage, have been legal since 1999.
Hollande has taken a more cautious approach to euthanasia, appointing a commission to study the issue first. A recent poll showed 49 percent of the French favoured assisted suicide.
While the two reforms were part of Hollande's election platform, they were not main issues in the campaign debate.
WHAT DOES THE PRAYER SAY?
The prayer first recalled the victims of the current economic crisis and expressed hope that elected officials would legislate with the common good in mind.
In the passage widely taken as an allusion to same-sex marriage and adoption, it said children should "cease to be objects of the desires and conflicts of adults and fully benefit from the love of a father and a mother".
The prayer also hoped for support for families "throughout their lives, especially in painful moments", a reference taken as criticism of any plan to legalise euthanasia.
The prayer was read out at Mass on Wednesday, the feast of the Assumption, when Catholics believe the Virgin Mary was assumed bodily into heaven. Assumption is a national holiday in traditionally Catholic but now largely secular France.
French media reported some priests had decided not to read out the prayer. Television and radio showed mixed opinions among Catholics leaving Mass, with some approving the prayer and others supporting the legalisation of same-sex marriage.
Civitas, a group of traditionalist Catholics that has criticised the French Church in the past for not speaking out more in public, has said it also plans to campaign against the coming legalisation of same-sex marriage.