The Catholic Church has taken its own vow of silence on two elite Catholic schools defying its authority and appearing to endorse same-sex marriage.

Archbishop of Melbourne Denis Hart on Wednesday declined to weigh in on remarks by St Ignatius’ College, Riverview and Xavier College last week that seemed to tacitly support gay marriage, while the Bishops Commission for Catholic Education also chose not to respond.

The prestigious Jesuit schools, which have educated some of the most powerful figures in politics, last week hit a strikingly sympathetic note on allowing same-sex couples to marry.

They called on the community to keep Christian teachings on love and acceptance in mind as well as conservative doctrine.

Archbishop Denis Hart has not tackled two elite schools on their public statement’s on same-sex marriage. Photo: Getty

While not explicitly calling for a “yes” vote in the postal plebiscite, Xavier College rector Chris Middleton said that Catholics should distinguish between morality and public policy, and that church teaching was out of synch with young people’s views on equality.

“For many Catholics engaged in the debate the critical question is whether the denial of the right to civil marriage is an ‘unjust discrimination’?” Father Middleton wrote on the Melbourne school’s website.

Ross Jones, rector at St Ignatius’ College in Sydney, similarly emphasised acceptance in the school newsletter, quoting Pope Francis’ remarks on being in no position to judge gay people.

“Presumably, same sex-couples, who make such a commitment to each other in good conscience, do so by reflecting on experience and on what it is to be human, using their God-given reason,” said Father Jones, who acknowledged not consulting with the church hierarchy before his remarks.

Past pupils are now key decision makers

The schools are two of the most prestigious fee-paying institutions in Australia, with a reputation for producing high flyers in politics and business.

St Ignatius’ College counts former prime minister Tony Abbott, Deputy Prime Minister Barnaby Joyce and former New South Wales premier Nick Greiner among its past pupils, while Xavier College’s alumni include Labor leader Bill Shorten.

The surprise comments came after Archbishop Hart was reported to have warned that staff at Catholic-run schools and hospitals could face the sack for marrying their same-sex partner if and when gay marriage is legalised.

The senior cleric later denied threatening to fire people for simply being in a same-sex union, but said that teachers at Catholic schools would be expected to continue teaching Catholic values.

The National Catholic Education Commission, which sits under the Bishops Commission for Catholic Education, has lobbied strongly for religious exemptions in any same-sex marriage legislation in order to “enshrine the right of all faith-based schools to teach their view of marriage, consistent with their conscientiously held religious beliefs”.

While church leaders are keeping quiet on the rebellion within their ranks, St Ignatius’ College on Wednesday riterated calls for Catholics to acknowledge the humanity of LGBTI Australians as well as its teachings on marriage.

“In forming a response to this issue, a properly formed and informed conscience would take into account both the teachings of the Church about the sacrament of marriage, as well as the teachings of the Church about human dignity, which of course includes LGBTI people,” the school said in a joint statement attributed to Fr Jones and school principal Paul Hine.

“A discerned response to these issues means holding all of these teachings together.”