The attackers also left a pamphlet in Santiago's Saint Elizabeth of Hungary church threatening Pope Francis.
Three Catholic churches were firebombed in the Chilean capital Santiago on Friday, days before the start of a visit to the country by Pope Francis.
President Michelle Bachelet condemned the incidents, which happened during the night and caused minor damage.
"It's very strange, because it's not something you can identify as a specific group," Bachelet said on national radio.
Police Chief Gonzalo Araya said "anarchist groups" may have been responsible.
Two of the churches suffered fire damage to doorways, while the wall of a third was scrawled with graffiti condemning the pope's visit.
The attackers left a pamphlet in the city's Saint Elizabeth of Hungary church threatening the pontiff.
"Pope Francis, the next bombs will be in your soutane," said the printed note, referring to a type of robe worn by Catholic clergy.
The note railed against Catholic Church "domination" of individuals.
"We will never submit to domination of our bodies, our ideas, and actions," it said.
Interior ministry official Mahmud Aleuy said the government was investigating the attacks.
The 81-year-old pontiff is due to arrive in Santiago on Monday evening at the start of a week-long visit to Chile and Peru.