The Pope veered off his script when speaking out about abuse, saying he had set out a "greater commitment to eliminating this scourge in the Church, at any cost".
With the reverberations of a litany of church sex abuse scandals casting a shadow over the first papal visit to Ireland in nearly 40 years, Francis confronted the issue in his address inside the castle's St Patrick's Hall.
In a statement issued after their meeting, Higgins said he "raised with His Holiness the vast suffering and hurt caused by child sex abuse perpetrated by some within the Catholic Church", as well as the "anger which had been conveyed to him at what was perceived to be the impunity enjoyed by those who had the responsibility of bringing such abuses for action by the appropriate authorities and have not done so".
Earlier this week, the pope wrote a 2,000-word letter to Catholics in which he condemned the crime of sexual abuse by priests and subsequent cover-ups.
"I can not fail to acknowledge the grave scandal caused in Ireland by the abuse of young people by members of the church charged with responsibility for their protection and education", Francis told a room filled with members of the Irish government, other lawmakers and diplomats.
Pope Francis marked the first papal visit to Ireland in 39 years by acknowledging that the failure of Church authorities to adequately address "repugnant" clerical child abuse crimes there remains a source of shame for the Catholic community. The reviews concluded that thousands of children were raped and molested by priests or physically abused in church-run schools and bishops worked for years to hide those crimes.
A Vatican spokesman had no comment on the details of what was said in the meeting.
And Ireland's church attendance has waned from 90% to about 30% as revelations of abuse by Catholic-run institutions continue to damage its moral authority and diminish its influence.
More than three-quarters of Ireland's population flocked to see Pope John Paul II in 1979 when divorce and contraception there were illegal.
Pope Francis during a tree planting ceremony with President of Ireland Michael D. Higgins (2nd R) and his wife Sabina Coyne (R) at Aras an Uachtarain on August 25, 2018 in Dublin, Ireland.
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"He is welcome as a guest but he is going to have to take action rather than repeat platitudes if we are really going to have any respect for the Church generally", said Helen Carey, a visual arts curator, walking past Dublin Castle where the state reception will be held.
"The Catholic Church is still very much part of our society but not at the centre of it as it was 40 years ago", Prime Minister Leo Varadkar, who last year became Ireland's first gay leader, told the BBC ahead of the visit.
He said Ireland's multiple historic scandals were "stains on our state, our society and also the Church".
Hundreds of thousands more will attend a Mass celebrated by the Pope at the city's Phoenix Park on Sunday afternoon, with all 500,000 tickets for the free event booked out.
Later, at St Mary's Pro Cathedral in Dublin, he held a silent prayer in front of a candle that commemorates abuse victims, before answering questions from couples of all ages on the subject of marriage.
He will begin the two-day visit by meeting Ireland's President Michael D. Higgins and Varadkar, who has promised to challenge the pope to do more in dealing with the abuse crisis.
Varadkar plans to tell the Pope that the exclusion of LGBT+ people from the Catholic Church "really hurts".
Some 600,000 people are expected to turn out to see the pope in both Dublin and Knock over the weekend.
In the evening, he will join pilgrims at a musical festival in the landmark Croke Park Gaelic Athletic Association stadium.