Tsunami waves of less than 1 metre (3 feet) were recorded in several areas of the Southeast Asian nation. The tsunami warning was lifted about three hours after the quake.
In addition to the deaths of at least two, one person was injured in Sikka Regency, the disaster mitigation agency BNPB said in a statement.
Parts of a building collapsed into dust and rubble as people screamed and ran in the street, a video on Facebook, verified by Reuters as being at a port in Maumere, showed. It is the main town in Sikka Regency on Flores Island in the east of Indonesia's vast archipelago.
Strong shaking was felt across East Nusa Tenggara, West Nusa Tenggara and parts of South Sulawesi, and residents in several areas reported shaking lasting about one minute, BNPB said.
"Most of the people felt the shock and scattered out of their homes," it said.

Villagers outside their homes following an earthquake of magnitude 7.7, in Talibura, Easu Nusa Tenggara, Indonesia August 15, 2026 this still image obtained from video. Photo: REUTERS
A hospital in the district of Ende in East Nusa Tenggara Province was moving patients outside, Kompas TV footage showed, and Kompas.com reported at least one landslide.
Geophysics agency BMKG recorded the first quake at 4:58 a.m. (2158 GMT) at a depth of 15 km (9 miles), followed by several aftershocks.
Australia's tsunami warning centre said the undersea earthquake would have "no tsunami threat to the Australian mainland, islands or territories".
Reuters
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