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".