Unknown vandals set fire to at least two churches, threw a homemade bomb at one and left pamphlets with threatening messages to the pontiff early on Friday morning, days before his arrival in the South American country. No one was injured, and no group has claimed responsibility for the attacks.
Fernandez told local radio station BioBio that small groups with limited capabilities were to blame, but he did not name them.
"These are serious and inexcusable actions, but we have to put things in perspective," he said. "We are not talking about significant groups that are truly dangerous."
Francis, who hails from Argentina and is the first Latin American pope, will arrive in Chile on Monday. A Mass he has planned to hold on Tuesday in a Santiago park is expected to attract more than 500,000 people.
Various groups are planning demonstrations on issues ranging from indigenous rights to a sexual abuse scandal.
The pope will also visit the cities of Temuco and Iquique before heading to Peru.
In Lima, an overnight fire at the foot of a 35-metre statue of Jesus Christ left the monument sooty on Saturday. Police said that was the result of an electrical failure, rather than an attack.
