The fire started late on Thursday in San Felipe, 90 kilometers (56 miles) northwest of capital Santiago, and also damaged four nearby homes, the Interior Ministry’s emergency office, ONEMI said.
Experts from the Forensic Medical Service were working to identify the deceased due to the conditions in which the bodies were found, officials said.
San Felipe fire commander Juan Carlos Herrera told reporters that the fire was already spreading inside the home when his team arrived at the scene.
Possible causes of the fire included an overheated gas cooker or electrical system, according to officials.
The fire completely destroyed the government-run shelter.