The agency said the epicentre of the quake was on land at a depth of 75 kilometres (46.6 miles), adding it was felt in Kupang, a city in the East Nusa Tenggara province on the western side of Timor island.
Christa Elim, a Kupang resident, said she and her husband ran out of a shophouse after feeling tremors.
"It was quite strong. I felt it twice like I was shoved off a chair," she said via telephone.
There were no immediate reports of damage. A spokesperson for Indonesia's disaster mitigation agency did not immediately respond to a request for comment.
Indonesia straddles the so-called "Pacific Ring of Fire", a highly seismically active zone, where different plates on the Earth's crust meet and create a large number of earthquakes and volcanic activity.
(Reporting by Stanley Widianto, Gayatri Suroyo, Fransiska Nangoy; Editing by Kanupriya Kapoor)
