The 7.6 magnitude quake, centered in Papua province, was felt as far away as Australia and sent small tsunamis washing into southern Japan.
Residents near the epicenter rushed from their homes to higher ground in fear of a large tsunami that might have been generated by the quake.
The U.S. Geological Survey said the temblor was centered about 95 miles (150 km) west-northwest of Paupa’s main city of Manokwari at a depth of about 20 miles (35 km).
Thousands of residents filled the roads out of that blacked-out city, heading away from the sea despite the tsunami warning being lifted.
The initial quake was felt for about three minutes, beginning at 4:44 a.m. local time. Indonesia's Meteorology and Geophysics Agency said Papua received 842 aftershocks during the first 29 hours after the first quake, including 54 that were stronger than magnitude 5.
The ongoing seismic activity, which continued for several days, kept about 14,000 frightened residents huddling in makeshift refugee camps, or camping outside their damaged or destroyed homes.