It hit the Flores region at a shallow depth of just 6.2 miles (10km) just before 6am local time (11pm UK time) – and was followed by several aftershocks.
At least two people have been killed and two others injured, with footage broadcast by local media showing patients being evacuated from hospitals.
Medics moved beds, IV stands and oxygen cylinders outdoors to adapt to emergency conditions.
Saturday morning’s incident caused panic in a region that is prone to deadly earthquakes.
Guidelbertus Tanga, the rector of St Peter Major Seminary in Sikka, said: “At least one priest suffered a broken leg after jumping from the second floor of a building during the quake.”
An earthquake that struck Flores in December 1992 caused a tsunami that killed about 2,500 people.
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