According to Catholic aid charity Aid to the Church in Need (ACN), demonstrators recently broke into the Church of the Assumption in Santiago and set fire to pews, statues and other sacred images, many of which were dragged out of the church to make barricades against police.
The church was also covered in satanic imagery and graffiti.
Following the attack, the parish priest, Fr Pedro Narbona, told parishioners "not to slip into the cycle of hatred that can only end up poisoning the souls".
He added: "The Church is built not so much out of physical materials, but rather of the living stones, which we [all] are... We are the living stones and this is the fundamental truth."
The attack on the Church of the Assumption, part of a spate of attacks on churches in Chile, came during protests sparked by the government of President Sebastian Pinera's decision to increase the prices of subway tickets.
ACN said a week earlier, on 1st November, there was another attempted attack on the Church of the Assumption but Fr Pedro called the fire brigade in time.
The charity added that The Church of Vera Cruz, Santiago, Vilparaiso Cathedral, and the parish of Saint Teresa of the Andes in Villa Alfredo Lorca, Punta Arenas, were also attacked over the past few weeks.
Maria Covarrubias, National Director ACN (Chile), said the charity is deeply concerned at spike in violence that has taken place in recent days.
"We ask your prayers at this difficult time for our ecclesiastical assistant and his parishioners, for peace in our country and that God may convert the hearts of those who have committed these lamentable acts," she said.
The protests have raged for over three weeks and have left at least 20 people dead.
The Chilean Red Cross estimates 2,500 have been injured.
Despite expressing sympathy with the protesters, the Catholic Bishops Conference of Chile condemned the attack, stating: "An attack on temples and places of prayer, without any respect for God or for those who believe in Him, causes us pain."
They added that violence "prevents us from giving the right amount of attention.
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