The quake struck at a depth of 36.1 kilometres (22.5 miles) on the west of Timor island near the city of Kupang, according to the US Geological Survey.
Indonesia's geophysics agency, or BMKG, said the quake had a higher magnitude of 6.6.
The tremor was strongly felt in Kupang on the island split between Indonesian territory in the west and the sovereign state of East Timor in the east, according to an AFP journalist, but no casualties were reported.
Debris had fallen from buildings in the city and some residents were forced to evacuate their homes.
"I was dizzy and at first I thought it was because I was running in the morning," said 40-year-old Kupang resident Yeri, who like many Indonesians goes by one name.
"I was shocked to see several residents running out of their houses because the earthquake was so strong."
Indonesia experiences frequent earthquakes due to its position on the Pacific "Ring of Fire", an arc of intense seismic activity that stretches from Japan through Southeast Asia and across the Pacific basin.
In November last year, a 5.6-magnitude quake hit the populous West Java province on the country's main island of Java, killing 602 people.
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