A group of about 20 people entered St Mary’s Pro Cathedral on Dublin’s Marlborough Street during Sunday morning’s 11am mass.
A livestreamed video shows the group holding placards with Palestinian flags and photos of children as they walk up the aisle during a hymn to applause from the congregation.
Speaking from the altar, Monsignor Lorcan O’Brien noted that the Irish people “haven’t been silent” about the conflict in Palestine as he asked the protesters to exit the church.
Addressing the group, he said: “To those of you who have come into our church at a most inappropriate time to make your protest, I just want to say that the Irish people haven’t been silent and that the Irish people have supported the voice and the actions of our government.
“I would also like you to know that the Catholic community living in Gaza are especially in our thoughts and in our prayers at this time as well as all the people of Gaza, and then Palestinians everywhere.
“We would be grateful now if you would please leave our church as we conclude our liturgy now that you have made your protest.”
The protest has been widely criticised by the Christian community online in the wake of Cardinal Pierbattista Pizzaballa’s visit to the parish of the Holy Family in Gaza this weekend.
The Latin Patriarch of Jerusalem greeted the small Christian community, who have taken refuge in the parish compound since Israel’s attacks began last October, and told them that “all the people of the world, not only Christians, are with you” during a homily.
He will enter Bethlehem on Christmas Eve to celebrate a mass in St Catherine’s Church with the community there.
It comes after a service in Armagh was interrupted by pro-Palestinian protesters in a similar fashion earlier this month.A group of around 30 "cross-community Christians” took to St Patrick's Cathedral with signs to "highlight the silence from the Catholic church on genocide in Palestine".
According to one demonstrator Deirdre Murphy Linder, the group held a "silent a dignified procession at the end of communion".
Speaking to the protesters during the service, Father Barry Mathews said the church is "not a political organisation, rather we are an organisation who trusts in God's plan and trusts God is present.”
He said that the work the Catholic church has done "for the care of children in Gaza" cannot be ignored.
"We here as a parish community have given £5,000 pounds from your donation,” Fr Matthews said.
"We don't use Mass as an opportunity for a quick snapshot. Let us not use the church for a place of political statement."