Two of Australia's most prestigious Catholic schools have cautiously endorsed same-sex marriage in messages to parents, staff and students, directly rebuking recent statements from church leaders.

While stopping short of advocating a "yes" vote, St Ignatius' College in Sydney and Xavier College in Melbourne appealed to Pope Francis' teachings on love, mercy and non-judgment, and urged the school community to dwell on their own consciences.

The two Jesuit schools have educated generations of Australian politicians. St Ignatius', which is independent of the Catholic system, is the alma mater of former prime minister Tony Abbott and Deputy Prime Minister Barnaby Joyce, while Opposition Leader Bill Shorten attended Xavier College.

Father Chris Middleton, rector of Xavier College, called on the church to reflect on the overwhelming support for marriage equality among young people, and cited an Irish archbishop who called for the church to take "a reality check".

"In my experience, there is almost total unanimity amongst the young in favour of same-sex marriage, and arguments against it have almost no impact on them," Father Middleton wrote.

"They are driven by a strong emotional commitment to equality, and this is surely something to respect and admire. They are idealistic in the value they ascribe to love, the primary gospel value."

The rector of St Ignatius', Father Ross Jones, outlined the rights already afforded to same-sex couples in Australia, adding many now wish to marry "for the same reasons as their opposite-sex counterparts".

Father Middleton also suggested the church exposed itself to charges of hypocrisy following the revelations of the Royal Commission into Institutional Responses to Child Sexual Abuse. Read more via Sydney Morning Herald