The Institute for Public Health said it had been sent 70 bats within the first week of January, three of which tested positive for rabies.
It said that while bats are active in spring and summer, there seemed to be more this January due to a heat wave.
Health officials said their presence in houses was "potentially risky".
There are 11 species of bats in Chile, some of which live very close to humans, the Institute of Health said in a statement [in Spanish] on its website.
In 1996, a seven-year-old boy died in the city of Rancagua after contracting rabies from a bat bite.
The most recent case of rabies in a human in Chile was in 2013, but that time the young man survived.
Veronica Yung of the rabies department at the Institute for Public Health advised people who found bats inside their homes to contact the authorities so that the animals can be caught and sent for testing.
If they test negative, they are released in an appropriate environment.
Ms Yung said that in cases in which the authorities were unavailable, people should use thick latex gloves and attempt to catch the animals under a container without touching them.
She said that the institute had received a growing number of calls from people who had found bats inside their homes.
There were even reports of bats being found during daylight hours, which she said was an "anomaly" as they are typically active at night.
Chilean media are speaking of "a plague" of bats based on the number of calls made to the authorities and the fact that the Institute for Public Health has been sent more than double the weekly average of bats for rabies testing compared to 2016.
Bats are protected under Chilean law and it is prohibited to hunt or kill them.
Chile's health authorities have warned people to be wary of an increasing number of bats appearing in homes across the country.