More than 1,000 homes in North Sulawesi province were damaged when the magnitude 7.5 quake struck at 1:02 a.m. local time.
Around 400 of the houses were leveled to the ground, Central Sulawesi Governor Bandjela Paliudju told reporters.
A tsunami alert was issued immediately following the quake, but no significant changes in sea level were detected over the following hour.
Still, more than 20,000 residents fled to the hills near their homes in the coastal Buol district, remaining there overnight in fear that the seismic ocean waves could strike without warning.
A series of sharp aftershocks followed the initial quake, with the strongest registering a magnitude of 6.0.
The ongoing seismic activity sparked further panic among residents and prevented them from returning to their homes.
The U.S. Geological Survey determined the epicenter of the temblor was 85 miles (135 km) northwest of the Sulawesi city of Gorontalo at a depth of 16 miles (26 km).