According to the Associated Press, 384 people have died after a magnitude 7.5 earthquake and its resulting tsunami .
Most of the dead are believed to be from the city of Palu, on the island of Sulawesi.
There are also fears for thousands of people who were believed to be at a beach festival at the time the tsunami struck land.
National Disaster Mitigation Agency spokesman Sutopo Purwo Nugroho said on Friday (local time) that houses were swept away and families are reported missing.
Palu airport was also closed.
Mr Nugroho said communications with the area in central Sulawesi are down, while the search and rescue effort was initially hampered by darkness.
While the earthquake had prompted a tsunami alert, the alert was lifted within an hour.
Earlier, a milder quake destroyed some houses, killing one person and injuring at least 10 in Donggala, authorities said.
More than 600,000 people live in Donggala and Palu.
"The [second] quake was felt very strongly, we expect more damage and more victims," Mr Nugroho said, adding that evacuation process is still ongoing.
Based on initial reports, "many buildings" collapsed due to the 7.5 magnitude quake , he said.
A series of earthquakes in July and August killed nearly 500 people on the holiday island of Lombok, hundreds of kilometres southwest of Sulawesi.
Indonesia sits on the Pacific Ring of Fire and is regularly hit by earthquakes.