Earlier in the day, the secretariat stated that one person had died in the province of Azuay.
"Three people died ... in the province of El Oro," the secretariat said, bringing the death toll from the earthquake to four.
A two-story building with people inside collapsed in El Oro, with a number of shops and a university also damaged, according to the emergency service.
An earthquake was reported at 17:12 GMT on Saturday at a depth of 80 kilometers (50 miles), with the epicenter located 59 kilometers north of the city of Machala, according to the the European Mediterranean Seismological Center.
Media also reported that several people had been injured and one victim was killed when their car was crushed by a collapsing wall in the city of Cuenca. The quake also caused structural damage in at least two other provinces in Ecuador and was felt in half of the country.
State-run oil company Petroecuador reportedly evacuated multiple facilities and halted production but has not yet reported any damage.