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Around 100 abortion rights protesters stormed Chile's Santiago Cathedral, damaging walls inside the building and disrupting service before clashing with police.
The trouble flared late Thursday after hardline members of a largely peaceful demonstration of 7,000 split away from the main protest and rushed into the cathedral.
Police later made two arrests in connection with the vandalism.
The assault on the cathedral was roundly condemned by Chilean government officials and members of the Catholic church on Friday.
"I wish to express our absolute rejection of such acts," Chile's President Sebastian Pinera said, vowing that government forces would "use the full force of the law against these delinquents."
The head of the Catholic Church in Chile, Archbishop of Santiago Ricardo Ezzati condemned the acts as "very serious."
He also blasted the "intolerance" of the protesters, accusing them of "violating freedom of religion and worship" by ransacking the cathedral, which will now be closed for five days as a clean-up operation gets under way.
Both the archdiocese and city of Santiago have filed legal complaints against those responsible for the damage.
Abortion was banned in Catholic-dominated Chile by former dictator Augusto Pinochet.
However several feminist organizations and politicians, including the socialist candidate for November 17 elections, Michelle Bachelet, have protested in favor of abortion being legal in cases of rape or when the mother's life is deemed to be at risk.
Chile's legislature has been unable to form a consensus on abortion in a deeply conservative country where divorce was only legalized in 2004.