The quake, which was 20 miles deep, was centered 15 miles off the coastal town of Champerico and 100 miles southwest of Guatemala City. It was the strongest earthquake to hit Guatemala since a 1976 temblor that killed 23,000.
Officials said most of 100 missing were from San Marcos, where people farm corn and herd cattle, mostly for their own survival.
Hospital officials in San Marcos said they had received 150 injured.
Perez said more than 2,000 soldiers were deployed to help with the disaster. A plane had made at least two trips to carry relief teams to the area.