In the overnight attacks in Santiago, the capital and largest city where the pope will arrive on Monday, the churches were hit with firebombs and then sprayed with accelerant. At one, the doors were burned before firefighters extinguished the blaze.
"The next bombs will be in your cassock," read pamphlets found outside one of the churches.
Later in the day, police found barrels of flammable liquid at two other churches that had not been ignited. They were handled by bomb squads without incident.
After the previously scheduled security meeting, Bachelet said the Andean nation of 17 million was prepared for the first papal visit since Saint John Paull II came in 1987.
"I also want to invite you all to experience this visit in a climate of respect, solidarity and happiness," Bachelet said.
There were no immediate arrests in the firebombings, and authorities downplayed their significance with Interior Ministry official Mahmud Aleuy calling the damage "minor."
Earlier this week police said 18,000 officers would be deployed during Francis' visits to Santiago, Temuco and the northern city of Iquique. Police will also have helicopters on hand and monitor events with drones.
It was unclear who might have been behind yesterday's attacks. A small minority of Mapuches have used violence to further their cause, and in recent years churches have been targeted.
Chile also has a handful of anarchist groups that periodically attack property and clash with police during protests.
Hugo Alcaman, president of ENAMA, a Mapuche group that encourages local businesses and advocates social change, condemned the attacks.
"We reject all types of violence, which we don't think is intelligent or effective," said Alcaman.
Francis' visit to Chile and Peru aims to highlight immigration, the suffering of indigenous peoples and protecting the Amazon rainforest.
However sex abuse in the Chilean church and political instability in Peru have become central themes as his arrival nears.
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